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1
Pang, Erli, and Kui Lin. "Yeast protein–protein interaction binding sites: prediction from the motif–motif, motif–domain and domain–domain levels." Molecular BioSystems 6, no. 11 (2010): 2164. http://dx.doi.org/10.1039/c0mb00038h.
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Millard, Peter S., Konrad Weber, Birthe B. Kragelund, and Meike Burow. "Specificity of MYB interactions relies on motifs in ordered and disordered contexts." Nucleic Acids Research 47, no. 18 (August 10, 2019): 9592–608. http://dx.doi.org/10.1093/nar/gkz691.
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Abstract Physical interactions between members of the MYB and bHLH transcription factor (TF) families regulate many important biological processes in plants. Not all reported MYB–bHLH interactions can be explained by the known binding sites in the R3 repeat of the MYB DNA-binding domain. Noteworthy, most of the sequence diversity of MYB TFs lies in their non-MYB regions, which contain orphan small subgroup-defining motifs not yet linked to molecular functions. Here, we identified the motif mediating interaction between MYB TFs from subgroup 12 and their bHLH partners. Unlike other known MYB–bHLH interactions, the motif locates to the centre of the predicted disordered non-MYB region. We characterised the core motif, which enabled accurate prediction of previously unknown bHLH-interacting MYB TFs in Arabidopsis thaliana, and we confirmed its functional importance in planta. Our results indicate a correlation between the MYB–bHLH interaction affinity and the phenotypic output controlled by the TF complex. The identification of an interaction motif outside R3 indicates that MYB–bHLH interactions must have arisen multiple times, independently and suggests many more motifs of functional relevance to be harvested from subgroup-specific studies.
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Lim, Jia Jia, Youngjin Lee, Tue Tu Ly, Jung Youn Kang, Jung-Gyu Lee, Jun Yop An, Hyung-Seop Youn, et al. "Structural insights into the interaction of p97 N-terminus domain and VBM in rhomboid protease, RHBDL4." Biochemical Journal 473, no. 18 (September 12, 2016): 2863–80. http://dx.doi.org/10.1042/bcj20160237.
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RHBDL4 is an active rhomboid that specifically recognizes and cleaves atypical, positively charged transmembrane endoplasmic reticulum-associated degradation (ERAD) substrates. Interaction of valosin-containing protein (p97/VCP) and RHBDL4 is crucial to retrotranslocate polyubiquitinated substrates for ERAD pathway. Here, we report the first complex structure of VCP-binding motif (VBM) with p97 N-terminal domain (p97N) at 1.88 Å resolution. Consistent with p97 adaptor proteins including p47-ubiquitin regulatory X (UBX), gp78-VCP-interacting motif (VIM), OTU1-UBX-like element, and FAF1-UBX, RHBDL4 VBM also binds at the interface between the two lobes of p97N. Notably, the RF residues in VBM are involved in the interaction with p97N, showing a similar interaction pattern with that of FPR signature motif in the UBX domain, although the directionality is opposite. Comparison of VBM interaction with VIM of gp78, another α-helical motif that interacts with p97N, revealed that the helix direction is inversed. Nevertheless, the conserved arginine residues in both motifs participate in the majority of the interface via extensive hydrogen bonds and ionic interactions with p97N. We identified novel VBM-binding mode to p97N that involves a combination of two types of p97–cofactor specificities observed in the UBX and VIM interactions. This highlights the induced fit model of p97N interdomain cleft upon cofactor binding to form stable p97–cofactor complexes. Our mutational and biochemical analyses in defining the specific interaction between VBM and p97N have elucidated the importance of the highly conserved VBM, applicable to other VBM-containing proteins. We also showed that RHBDL4, ubiquitins, and p97 co-operate for efficient substrate dislocation.
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Nielsen, Anders Lade, Poul Jørgensen, Thierry Lerouge, Margarita Cerviño, Pierre Chambon, and Régine Losson. "Nizp1, a Novel Multitype Zinc Finger Protein That Interacts with the NSD1 Histone Lysine Methyltransferase through a Unique C2HR Motif." Molecular and Cellular Biology 24, no. 12 (June 15, 2004): 5184–96. http://dx.doi.org/10.1128/mcb.24.12.5184-5196.2004.
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ABSTRACT Haploinsufficiency of the NSD1 gene is a hallmark of Sotos syndrome, and rearrangements of this gene by translocation can cause acute myeloid leukemia. The NSD1 gene product is a SET-domain histone lysine methyltransferase that has previously been shown to interact with nuclear receptors. We describe here a novel NSD1-interacting protein, Nizp1, that contains a SCAN box, a KRAB-A domain, and four consensus C2H2-type zinc fingers preceded by a unique finger derivative, referred to herein as the C2HR motif. The C2HR motif functions to mediate protein-protein interaction with the cysteine-rich (C5HCH) domain of NSD1 in a Zn(II)-dependent fashion, and when tethered to RNA polymerase II promoters, represses transcription in an NSD1-dependent manner. Mutations of the cysteine or histidine residues in the C2HR motif abolish the interaction of Nizp1 with NSD1 and compromise the ability of Nizp1 to repress transcription. Interestingly, converting the C2HR motif into a canonical C2H2 zinc finger has a similar effect. Thus, Nizp1 contains a novel type of zinc finger motif that functions as a docking site for NSD1 and is more than just a degenerate evolutionary remnant of a C2H2 motif.
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Bardwell, V. J., and R. Treisman. "The POZ domain: a conserved protein-protein interaction motif." Genes & Development 8, no. 14 (July 15, 1994): 1664–77. http://dx.doi.org/10.1101/gad.8.14.1664.
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He, Bin, and Elizabeth M. Wilson. "Electrostatic Modulation in Steroid Receptor Recruitment of LXXLL and FXXLF Motifs." Molecular and Cellular Biology 23, no. 6 (March 15, 2003): 2135–50. http://dx.doi.org/10.1128/mcb.23.6.2135-2150.2003.
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ABSTRACT Coactivator recruitment by activation function 2 (AF2) in the steroid receptor ligand binding domain takes place through binding of an LXXLL amphipathic α-helical motif at the AF2 hydrophobic surface. The androgen receptor (AR) and certain AR coregulators are distinguished by an FXXLF motif that interacts selectively with the AR AF2 site. Here we show that LXXLL and FXXLF motif interactions with steroid receptors are modulated by oppositely charged residues flanking the motifs and charge clusters bordering AF2 in the ligand binding domain. An increased number of charged residues flanking AF2 in the ligand binding domain complement the two previously characterized charge clamp residues in coactivator recruitment. The data suggest a model whereby coactivator recruitment to the receptor AF2 surface is initiated by complementary charge interactions that reflect a reversal of the acidic activation domain-coactivator interaction model.
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Pascoe, Heath G., Stephen Gutowski, Hua Chen, Chad A. Brautigam, Zhe Chen, Paul C. Sternweis, and Xuewu Zhang. "Secondary PDZ domain-binding site on class B plexins enhances the affinity for PDZ–RhoGEF." Proceedings of the National Academy of Sciences 112, no. 48 (November 16, 2015): 14852–57. http://dx.doi.org/10.1073/pnas.1508931112.
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PDZ domains are abundant protein interaction modules and typically recognize a short motif at the C terminus of their ligands, with a few residues in the motif endowing the binding specificity. The sequence-based rules, however, cannot fully account for the specificity between the vast number of PDZ domains and ligands in the cell. Plexins are transmembrane receptors that regulate processes such as axon guidance and angiogenesis. Two related guanine nucleotide exchange factors (GEFs), PDZ–RhoGEF and leukemia-associated RhoGEF (LARG), use their PDZ domains to bind class B plexins and play critical roles in signaling. Here, we present the crystal structure of the full-length cytoplasmic region of PlexinB2 in complex with the PDZ domain of PDZ–RhoGEF. The structure reveals that, in addition to the canonical C-terminal motif/PDZ interaction, the 3D domain of PlexinB2 forms a secondary interface with the PDZ domain. Our biophysical and cell-based assays show that the secondary interface contributes to the specific interaction between plexin and PDZ–RhoGEF and to signaling by plexin in the cell. Formation of secondary interfaces may be a general mechanism for increasing affinity and specificity of modular domain-mediated interactions.
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Litvinov, Rustem I., Marco Mravic, Hua Zhu, John W. Weisel, William F. DeGrado, and Joel S. Bennett. "Unique transmembrane domain interactions differentially modulate integrin αvβ3 and αIIbβ3 function." Proceedings of the National Academy of Sciences 116, no. 25 (June 3, 2019): 12295–300. http://dx.doi.org/10.1073/pnas.1904867116.
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Lateral transmembrane (TM) helix–helix interactions between single-span membrane proteins play an important role in the assembly and signaling of many cell-surface receptors. Often, these helices contain two highly conserved yet distinct interaction motifs, arranged such that the motifs cannot be engaged simultaneously. However, there is sparse experimental evidence that dual-engagement mechanisms play a role in biological signaling. Here, we investigate the function of the two conserved interaction motifs in the TM domain of the integrin β3-subunit. The first motif uses reciprocating “large-large-small” amino acid packing to mediate the interaction of the β3 and αIIb TM domains and maintain the inactive resting conformation of the platelet integrin αIIbβ3. The second motif, S-x3-A-x3-I, is a variant of the classical “G-x3-G” motif. Using site-directed mutagenesis, optical trap-based force spectroscopy, and molecular modeling, we show that S-x3-A-x3-I does not engage αIIb but rather mediates the interaction of the β3 TM domain with the TM domain of the αv-subunit of the integrin αvβ3. Like αIIbβ3, αvβ3 on circulating platelets is inactive, and in the absence of platelet stimulation is unable to interact with components of the subendothelial matrix. However, disrupting any residue in the β3 S-x3-A-x3-I motif by site-directed mutations is sufficient to induce αvβ3 binding to the αvβ3 ligand osteopontin and to the monoclonal antibody WOW-1. Thus, the β3-integrin TM domain is able to engage in two mutually exclusive interactions that produce alternate α-subunit pairing, creating two integrins with distinct biological functions.
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Brady, Troy L., Peter G. Fuerst, Robert A. Dick, Clarice Schmidt, and Daniel F. Voytas. "Retrotransposon Target Site Selection by Imitation of a Cellular Protein." Molecular and Cellular Biology 28, no. 4 (December 17, 2007): 1230–39. http://dx.doi.org/10.1128/mcb.01502-07.
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ABSTRACT Mobile elements rely on cellular processes to replicate, and therefore, mobile element proteins frequently interact with a variety of cellular factors. The integrase (IN) encoded by the retrotransposon Ty5 interacts with the heterochromatin protein Sir4, and this interaction determines Ty5's preference to integrate into heterochromatin. We explored the hypothesis that Ty5's targeting mechanism arose by mimicking an interaction between Sir4 and another cellular protein(s). Mutational analyses defined the requirements for the IN-Sir4 interaction, providing criteria to screen for cellular analogues. Esc1, a protein associated with the inner nuclear membrane, interacted with the same domain of Sir4 as IN, and 75% of mutations that disrupted IN-Sir4 interactions also abrogated Esc1-Sir4 interactions. A small motif critical for recognizing Sir4 was identified in Esc1. The functional equivalency of this motif and the Sir4-interacting domain of IN was demonstrated by swapping these motifs and showing that the chimeric IN and Esc1 proteins effectively target integration and partition DNA, respectively. We conclude that Ty5 targets integration by imitating the Esc1-Sir4 interaction and suggest molecular mimicry as a general mechanism that enables mobile elements to interface with cellular processes.
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Gurung, Raju, Darlami Om, Rabin Pun, Soonsil Hyun, and Dongyun Shin. "Recent Progress in Modulation of WD40-Repeat Domain 5 Protein (WDR5): Inhibitors and Degraders." Cancers 15, no. 15 (August 1, 2023): 3910. http://dx.doi.org/10.3390/cancers15153910.
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WD40-repeat (WDR) domain proteins play a crucial role in mediating protein–protein interactions that sustain oncogenesis in human cancers. One prominent example is the interaction between the transcription factor MYC and its chromatin co-factor, WD40-repeat domain protein 5 (WDR5), which is essential for oncogenic processes. The MYC family of proteins is frequently overexpressed in various cancers and has been validated as a promising target for anticancer therapies. The recruitment of MYC to chromatin is facilitated by WDR5, highlighting the significance of their interaction. Consequently, inhibiting the MYC–WDR5 interaction has been shown to induce the regression of malignant tumors, offering an alternative approach to targeting MYC in the development of anticancer drugs. WDR5 has two protein interaction sites, the “WDR5-binding motif” (WBM) site for MYC interaction and the histone methyltransferases SET1 recognition motif “WDR5-interacting” (WIN) site forming MLL complex. Significant efforts have been dedicated to the discovery of inhibitors that target the WDR5 protein. More recently, the successful application of targeted protein degradation technology has enabled the removal of WDR5. This breakthrough has opened up new avenues for inhibiting the interaction between WDR5 and the binding partners. In this review, we address the recent progress made in targeting WDR5 to inhibit MDR5–MYC and MDR5–MLL1 interactions, including its targeted protein degradation and their potential impact on anticancer drug discovery.
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Chen, Zhuoyao, Gregory A. Wasney, Sarah Picaud, Panagis Filippakopoulos, Masoud Vedadi, Vincenzo D'Angiolella, and Alex N. Bullock. "Identification of a PGXPP degron motif in dishevelled and structural basis for its binding to the E3 ligase KLHL12." Open Biology 10, no. 6 (June 2020): 200041. http://dx.doi.org/10.1098/rsob.200041.
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Wnt signalling is dependent on dishevelled proteins (DVL1-3), which assemble an intracellular Wnt signalosome at the plasma membrane. The levels of DVL1-3 are regulated by multiple Cullin-RING E3 ligases that mediate their ubiquitination and degradation. The BTB-Kelch protein KLHL12 was the first E3 ubiquitin ligase to be identified for DVL1-3, but the molecular mechanisms determining its substrate interactions have remained unknown. Here, we mapped the interaction of DVL1-3 to a ‘PGXPP' motif that is conserved in other known partners and substrates of KLHL12, including PLEKHA4, PEF1, SEC31 and DRD4. To determine the binding mechanism, we solved a 2.4 Å crystal structure of the Kelch domain of KLHL12 in complex with a DVL1 peptide that bound with low micromolar affinity. The DVL1 substrate adopted a U-shaped turn conformation that enabled hydrophobic interactions with all six blades of the Kelch domain β-propeller. In cells, the mutation or deletion of this motif reduced the binding and ubiquitination of DVL1 and increased its stability confirming this sequence as a degron motif for KLHL12 recruitment. These results define the molecular mechanisms determining DVL regulation by KLHL12 and establish the KLHL12 Kelch domain as a new protein interaction module for a novel proline-rich motif.
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Shi, Xiaoli, Sandrine Opi, Adrien Lugari, Audrey Restouin, Thibault Coursindel, Isabelle Parrot, Javier Perez, et al. "Identification and biophysical assessment of the molecular recognition mechanisms between the human haemopoietic cell kinase Src homology domain 3 and ALG-2-interacting protein X." Biochemical Journal 431, no. 1 (September 14, 2010): 93–102. http://dx.doi.org/10.1042/bj20100314.
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SFKs (Src family kinases) are central regulators of many signalling pathways. Their functions are tightly regulated through SH (Src homology) domain-mediated protein–protein interactions. A yeast two-hybrid screen using SH3 domains as bait identified Alix [ALG-2 (apoptosis-linked gene 2)-interacting protein X] as a novel Hck (haemopoietic cell kinase) SH3 domain interactor. The Alix–Hck-SH3 interaction was confirmed in vitro by a GST (glutathione transferase) pull-down assay and in intact cells by a mammalian two-hybrid assay. Furthermore, the interaction was demonstrated to be biologically relevant in cells. Through biophysical experiments, we then identified the PRR (proline-rich region) motif of Alix that binds Hck-SH3 and determined a dissociation constant of 34.5 μM. Heteronuclear NMR spectroscopy experiments were used to map the Hck-SH3 residues that interact with an ALIX construct containing the V and PRR domains or with the minimum identified interacting motif. Finally, SAXS (small-angle X-ray scattering) analysis showed that the N-terminal PRR of Alix is unfolded, at least before Hck-SH3 recognition. These results indicate that residues outside the canonical PxxP motif of Alix enhance its affinity and selectivity towards Hck-SH3. The structural framework of the Hck–Alix interaction will help to clarify how Hck and Alix assist during virus budding and cell-surface receptor regulation.
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Cuppen, Edwin, Herlinde Gerrits, Barry Pepers, Bé Wieringa, and Wiljan Hendriks. "PDZ Motifs in PTP-BL and RIL Bind to Internal Protein Segments in the LIM Domain Protein RIL." Molecular Biology of the Cell 9, no. 3 (March 1998): 671–83. http://dx.doi.org/10.1091/mbc.9.3.671.
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The specificity of protein–protein interactions in cellular signaling cascades is dependent on the sequence and intramolecular location of distinct amino acid motifs. We used the two-hybrid interaction trap to identify proteins that can associate with the PDZ motif-rich segment in the protein tyrosine phosphatase PTP-BL. A specific interaction was found with the Lin-11, Isl-1, Mec-3 (LIM) domain containing protein RIL. More detailed analysis demonstrated that the binding specificity resides in the second and fourth PDZ motif of PTP-BL and the LIM domain in RIL. Immunohistochemistry on various mouse tissues revealed a submembranous colocalization of PTP-BL and RIL in epithelial cells. Remarkably, there is also an N-terminal PDZ motif in RIL itself that can bind to the RIL-LIM domain. We demonstrate here that the RIL-LIM domain can be phosphorylated on tyrosine in vitro and in vivo and can be dephosphorylated in vitro by the PTPase domain of PTP-BL. Our data point to the presence of a double PDZ-binding interface on the RIL-LIM domain and suggest tyrosine phosphorylation as a regulatory mechanism for LIM-PDZ associations in the assembly of multiprotein complexes. These findings are in line with an important role of PDZ-mediated interactions in the shaping and organization of submembranous microenvironments of polarized cells.
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Santoso, Sentot, Valeria V. Orlova, Kaimei Song, Ulrich J. Sachs, Cornelia L. Andrei-Selmer, and Triantafyllos Chavakis. "The Homophilic Binding of Junctional Adhesion Molecule-C Mediates Tumor Cell-Endothelial Cell Interactions." Journal of Biological Chemistry 280, no. 43 (August 23, 2005): 36326–33. http://dx.doi.org/10.1074/jbc.m505059200.
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The junctional adhesion molecule C (JAM-C) was recently shown to undergo a heterophilic interaction with the leukocyte β2 integrin Mac-1, thereby mediating interactions between vascular cells in inflammatory cell recruitment. Here, the homophilic interaction of JAM-C is presented and functionally characterized to mediate tumor cell-endothelial cell interactions. Recombinant soluble JAM-C in fluid phase bound to immobilized JAM-C as assessed in a purified system; moreover, JAM-C-transfected Chinese hamster ovary (CHO) cells adhered to immobilized JAM-C. The homophilic interaction of JAM-C was mediated by the isolated amino-terminal Ig domain (D1), but not the carboxyl-terminal Ig domain (D2), of the molecule. Dimerization of JAM-A is dependent on the sequence RVE in the amino-terminal Ig domain. This motif is conserved in JAM-C (Arg64-Ile65-Glu66), and a single amino acid mutation in this motif (E66R) abolished the homophilic interaction of JAM-C. The lung carcinoma cell line NCI-H522 was found to express JAM-C. NCI-H522 cells adhered to immobilized JAM-C, as well as to JAM-C-transfected CHO cells, but not to mock-transfected CHO cells or to CHO cells transfected with the JAM-C mutant (E66R). Adhesion of NCI-H522 cells to JAM-C protein or JAM-C-transfected CHO cells was abolished in the presence of soluble JAM-C or the isolated D1. Furthermore, the adhesion of NCI-H522 cells to endothelial cells was significantly blocked by soluble JAM-C or the isolated D1. Thus, JAM-C undergoes a homophilic interaction via the Arg64-Ile65-Glu66 motif on the membrane-distal Ig domain of the molecule. The homophilic interaction of JAM-C can mediate tumor cell-endothelial cell interactions and may thereby be involved in the process of tumor cell metastasis.
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Guo, Yusong, Vasu Punj, Debrup Sengupta, and Adam D. Linstedt. "Coat-Tether Interaction in Golgi Organization." Molecular Biology of the Cell 19, no. 7 (July 2008): 2830–43. http://dx.doi.org/10.1091/mbc.e07-12-1236.
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Biogenesis of the Golgi apparatus is likely mediated by the COPI vesicle coat complex, but the mechanism is poorly understood. Modeling of the COPI subunit βCOP based on the clathrin adaptor AP2 suggested that the βCOP C terminus forms an appendage domain with a conserved FW binding pocket motif. On gene replacement after knockdown, versions of βCOP with a mutated FW motif or flanking basic residues yielded a defect in Golgi organization reminiscent of that occurring in the absence of the vesicle tether p115. Indeed, βCOP bound p115, and this depended on the βCOP FW motif. Furthermore, the interaction depended on E19E21 in the p115 head domain and inverse charge substitution blocked Golgi biogenesis in intact cells. Finally, Golgi assembly in permeabilized cells was significantly reduced by inhibitors containing intact, but not mutated, βCOP FW or p115 EE motifs. Thus, Golgi organization depends on mutually interacting domains in βCOP and p115, suggesting that vesicle tethering at the Golgi involves p115 binding to the COPI coat.
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Crowe, Brandon L., Ross C. Larue, Chunhua Yuan, Sonja Hess, Mamuka Kvaratskhelia, and Mark P. Foster. "Structure of the Brd4 ET domain bound to a C-terminal motif from γ-retroviral integrases reveals a conserved mechanism of interaction." Proceedings of the National Academy of Sciences 113, no. 8 (February 8, 2016): 2086–91. http://dx.doi.org/10.1073/pnas.1516813113.
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The bromodomain and extraterminal domain (BET) protein family are promising therapeutic targets for a range of diseases linked to transcriptional activation, cancer, viral latency, and viral integration. Tandem bromodomains selectively tether BET proteins to chromatin by engaging cognate acetylated histone marks, and the extraterminal (ET) domain is the focal point for recruiting a range of cellular and viral proteins. BET proteins guide γ-retroviral integration to transcription start sites and enhancers through bimodal interaction with chromatin and the γ-retroviral integrase (IN). We report the NMR-derived solution structure of the Brd4 ET domain bound to a conserved peptide sequence from the C terminus of murine leukemia virus (MLV) IN. The complex reveals a protein–protein interaction governed by the binding-coupled folding of disordered regions in both interacting partners to form a well-structured intermolecular three-stranded β sheet. In addition, we show that a peptide comprising the ET binding motif (EBM) of MLV IN can disrupt the cognate interaction of Brd4 with NSD3, and that substitutions of Brd4 ET residues essential for binding MLV IN also impair interaction of Brd4 with a number of cellular partners involved in transcriptional regulation and chromatin remodeling. This suggests that γ-retroviruses have evolved the EBM to mimic a cognate interaction motif to achieve effective integration in host chromatin. Collectively, our findings identify key structural features of the ET domain of Brd4 that allow for interactions with both cellular and viral proteins.
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Kimura, Yoko, Mirai Tanigawa, Junko Kawawaki, Kenji Takagi, Tsunehiro Mizushima, Tatsuya Maeda, and Keiji Tanaka. "Conserved Mode of Interaction between Yeast Bro1 Family V Domains and YP(X) n L Motif-Containing Target Proteins." Eukaryotic Cell 14, no. 10 (July 6, 2015): 976–82. http://dx.doi.org/10.1128/ec.00091-15.
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ABSTRACT Yeast Bro1 and Rim20 belong to a family of proteins which possess a common architecture of Bro1 and V domains. Alix and His domain protein tyrosine phosphatase (HD-PTP), mammalian Bro1 family proteins, bind YP(X) n L ( n = 1 to 3) motifs in their target proteins through their V domains. In Alix, the Phe residue, which is located in the hydrophobic groove of the V domain, is critical for binding to the YP(X) n L motif. Although the overall sequences are not highly conserved between mammalian and yeast V domains, we show that the conserved Phe residue in the yeast Bro1 V domain is important for binding to its YP(X) n L-containing target protein, Rfu1. Furthermore, we show that Rim20 binds to its target protein Rim101 through the interaction between the V domain of Rim20 and the YPIKL motif of Rim101. The mutation of either the critical Phe residue in the Rim20 V domain or the YPIKL motif of Rim101 affected the Rim20-mediated processing of Rim101. These results suggest that the interactions between V domains and YP(X) n L motif-containing proteins are conserved from yeast to mammalian cells. Moreover, the specificities of each V domain to their target protein suggest that unidentified elements determine the binding specificity.
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Gustafson, T. A., W. He, A. Craparo, C. D. Schaub, and T. J. O'Neill. "Phosphotyrosine-dependent interaction of SHC and insulin receptor substrate 1 with the NPEY motif of the insulin receptor via a novel non-SH2 domain." Molecular and Cellular Biology 15, no. 5 (May 1995): 2500–2508. http://dx.doi.org/10.1128/mcb.15.5.2500.
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The SHC proteins have been implicated in insulin receptor (IR) signaling. In this study, we used the sensitive two-hybrid assay of protein-protein interaction to demonstrate that SHC interacts directly with the IR. The interaction is mediated by SHC amino acids 1 to 238 and is therefore independent of the Src homology 2 domain. The interaction is dependent upon IR autophosphorylation, since the interaction is eliminated by mutation of the IR ATP-binding site. In addition, mutational analysis of the Asn-Pro-Glu-Tyr (NPEY) motif within the juxtamembrane domain of the IR showed the importance of the Asn, Pro, and Tyr residues to both SHC and IR substrate 1 (IRS-1) binding. We conclude that SHC interacts directly with the IR and that phosphorylation of Tyr-960 within the IR juxtamembrane domain is necessary for efficient interaction. This interaction is highly reminiscent of that of IRS-1 with the IR, and we show that the SHC IR-binding domain can substitute for that of IRS-1 in yeast and COS cells. We identify a homologous region within the IR-binding domains of SHC and IRS-1, which we term the SAIN (SHC and IRS-1 NPXY-binding) domain, which may explain the basis of these interactions. The SAIN domain appears to represent a novel motif which is able to interact with autophosphorylated receptors such as the IR.
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Elengoe, Asita, Mohammed Abu Naser, and Salehhuddin Hamdan. "A Novel Protein Interaction between Nucleotide Binding Domain of Hsp70 and p53 Motif." International Journal of Genomics 2015 (2015): 1–6. http://dx.doi.org/10.1155/2015/391293.
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Currently, protein interaction ofHomo sapiensnucleotide binding domain (NBD) of heat shock 70 kDa protein (PDB: 1HJO) with p53 motif remains to be elucidated. The NBD-p53 motif complex enhances the p53 stabilization, thereby increasing the tumor suppression activity in cancer treatment. Therefore, we identified the interaction between NBD and p53 using STRING version 9.1 program. Then, we modeled the three-dimensional structure of p53 motif through homology modeling and determined the binding affinity and stability of NBD-p53 motif complex structure via molecular docking and dynamics (MD) simulation. Human DNA binding domain of p53 motif (SCMGGMNR) retrieved from UniProt (UniProtKB: P04637) was docked with the NBD protein, using the Autodock version 4.2 program. The binding energy and intermolecular energy for the NBD-p53 motif complex were −0.44 Kcal/mol and −9.90 Kcal/mol, respectively. Moreover, RMSD, RMSF, hydrogen bonds, salt bridge, and secondary structure analyses revealed that the NBD protein had a strong bond with p53 motif and the protein-ligand complex was stable. Thus, the current data would be highly encouraging for designing Hsp70 structure based drug in cancer therapy.
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Yeung, Heidi O., Patrik Kloppsteck, Hajime Niwa, Rivka L. Isaacson, Steve Matthews, Xiaodong Zhang, and Paul S. Freemont. "Insights into adaptor binding to the AAA protein p97." Biochemical Society Transactions 36, no. 1 (January 22, 2008): 62–67. http://dx.doi.org/10.1042/bst0360062.
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The AAA (ATPase associated with various cellular activities) p97 [also known as VCP (valosin-containing protein)] participates in numerous biological activities and is an essential component of the ubiquitin signalling pathway. A plethora of adaptors have been reported for p97, and increasing evidence is suggesting that it is through adaptor binding that p97 is diverted into different cellular pathways. Studying the interaction between p97 and its adaptors is therefore crucial to our understanding of the physiological roles of the protein. The interactions between p97 and the PUB [PNGase (peptide N-glycosidase)/ubiquitin-associated] domain of PNGase, the UBX (ubiquitin regulatory X) domain of p47, and the UBD (ubiquitin D) domain of Npl4 have been structurally characterized. UBX and UBD are structural homologues that share similar p97-binding modes; it is plausible that other proteins that contain a UBX/UBX-like domain also interact with p97 via similar mechanisms. In addition, several short p97-interacting motifs, such as VBM (VCP-binding motif), VIM (VCP-interacting motif) and SHP, have been identified recently and are also shared between p97 adaptors, hinting that proteins possessing the same p97-binding motif might also share common p97-binding mechanisms. In this review, we aim to summarize our current knowledge on adaptor binding to p97.
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Loers, Gabriele, Ralf Kleene, Viviana Granato, Ute Bork, and Melitta Schachner. "Interaction of L1CAM with LC3 Is Required for L1-Dependent Neurite Outgrowth and Neuronal Survival." International Journal of Molecular Sciences 24, no. 15 (August 7, 2023): 12531. http://dx.doi.org/10.3390/ijms241512531.
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The neural cell adhesion molecule L1 (also called L1CAM or CD171) functions not only in cell migration, but also in cell survival, differentiation, myelination, neurite outgrowth, and signaling during nervous system development and in adults. The proteolytic cleavage of L1 in its extracellular domain generates soluble fragments which are shed into the extracellular space and transmembrane fragments that are internalized into the cell and transported to various organelles to regulate cellular functions. To identify novel intracellular interaction partners of L1, we searched for protein–protein interaction motifs and found two potential microtubule-associated protein 1 light-chain 3 (LC3)-interacting region (LIR) motifs within L1, one in its extracellular domain and one in its intracellular domain. By ELISA, immunoprecipitation, and proximity ligation assay using L1 mutant mice lacking the 70 kDa L1 fragment (L1-70), we showed that L1-70 interacts with LC3 via the extracellular LIR motif in the fourth fibronectin type III domain, but not by the motif in the intracellular domain. The disruption of the L1-LC3 interaction reduces L1-mediated neurite outgrowth and neuronal survival.
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Zhang, Feng, Jiyuan Ke, Li Zhang, Rongzhi Chen, Koichi Sugimoto, Gregg A. Howe, H. Eric Xu, Mingguo Zhou, Sheng Yang He, and Karsten Melcher. "Structural insights into alternative splicing-mediated desensitization of jasmonate signaling." Proceedings of the National Academy of Sciences 114, no. 7 (January 30, 2017): 1720–25. http://dx.doi.org/10.1073/pnas.1616938114.
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Jasmonate ZIM-domain (JAZ) transcriptional repressors play a key role in regulating jasmonate (JA) signaling in plants. Below a threshold concentration of jasmonoyl isoleucine (JA-Ile), the active form of JA, the C-terminal Jas motif of JAZ proteins binds MYC transcription factors to repress JA signaling. With increasing JA-Ile concentration, the Jas motif binds to JA-Ile and the COI1 subunit of the SCFCOI1 E3 ligase, which mediates ubiquitination and proteasomal degradation of JAZ repressors, resulting in derepression of MYC transcription factors. JA signaling subsequently becomes desensitized, in part by feedback induction of JAZ splice variants that lack the C-terminal Jas motif but include an N-terminal cryptic MYC-interaction domain (CMID). The CMID sequence is dissimilar to the Jas motif and is incapable of recruiting SCFCOI1, allowing CMID-containing JAZ splice variants to accumulate in the presence of JA and to re-repress MYC transcription factors as an integral part of reestablishing signal homeostasis. The mechanism by which the CMID represses MYC transcription factors remains elusive. Here we describe the crystal structure of the MYC3–CMIDJAZ10 complex. In contrast to the Jas motif, which forms a single continuous helix when bound to MYC3, the CMID adopts a loop–helix–loop–helix architecture with modular interactions with both the Jas-binding groove and the backside of the Jas-interaction domain of MYC3. This clamp-like interaction allows the CMID to bind MYC3 tightly and block access of MED25 (a subunit of the Mediator coactivator complex) to the MYC3 transcriptional activation domain, shedding light on the enigmatic mechanism by which JAZ splice variants desensitize JA signaling.
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Deltour, Sophie, Sébastien Pinte, Cateline Guerardel, Bohdan Wasylyk, and Dominique Leprince. "The Human Candidate Tumor Suppressor Gene HIC1 Recruits CtBP through a Degenerate GLDLSKK Motif." Molecular and Cellular Biology 22, no. 13 (July 1, 2002): 4890–901. http://dx.doi.org/10.1128/mcb.22.13.4890-4901.2002.
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ABSTRACT HIC1 (hypermethylated in cancer) and its close relative HRG22 (HIC1-related gene on chromosome 22) encode transcriptional repressors with five C2H2 zinc fingers and an N-terminal BTB/POZ autonomous transcriptional repression domain that is unable to recruit histone deacetylases (HDACs). Alignment of the HIC1 and HRG22 proteins from various species highlighted a perfectly conserved GLDLSKK/R motif highly related to the consensus CtBP interaction motif (PXDLSXK/R), except for the replacement of the virtually invariant proline by a glycine. HIC1 strongly interacts with mCtBP1 both in vivo and in vitro through this conserved GLDLSKK motif, thus extending the CtBP consensus binding site. The BTB/POZ domain does not interact with mCtBP1, but the dimerization of HIC1 through this domain is required for the interaction with mCtBP1. When tethered to DNA by fusion with the Gal4 DNA-binding domain, the HIC1 central region represses transcription through interactions with CtBP in a trichostatin A-sensitive manner. In conclusion, our results demonstrate that HIC1 mediates transcriptional repression by both HDAC-independent and HDAC-dependent mechanisms and show that CtBP is a HIC1 corepressor that is recruited via a variant binding site.
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Martin-Eauclaire, Marie-France, Géraldine Ferracci, Frank Bosmans, and Pierre E. Bougis. "A surface plasmon resonance approach to monitor toxin interactions with an isolated voltage-gated sodium channel paddle motif." Journal of General Physiology 145, no. 2 (January 26, 2015): 155–62. http://dx.doi.org/10.1085/jgp.201411268.
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Animal toxins that inhibit voltage-gated sodium (Nav) channel fast inactivation can do so through an interaction with the S3b–S4 helix-turn-helix region, or paddle motif, located in the domain IV voltage sensor. Here, we used surface plasmon resonance (SPR), an optical approach that uses polarized light to measure the refractive index near a sensor surface to which a molecule of interest is attached, to analyze interactions between the isolated domain IV paddle and Nav channel–selective α-scorpion toxins. Our SPR analyses showed that the domain IV paddle can be removed from the Nav channel and immobilized on sensor chips, and suggest that the isolated motif remains susceptible to animal toxins that target the domain IV voltage sensor. As such, our results uncover the inherent pharmacological sensitivities of the isolated domain IV paddle motif, which may be exploited to develop a label-free SPR approach for discovering ligands that target this region.
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Gupta, Anjali Bansal, Somsubhro Mukherjee, Catherine Quirong Pan, Adrian Velazquez-Campoy, J. Sivaraman, and Boon Chuan Low. "Spatial arrangement of LD motif-interacting residues on focal adhesion targeting domain of Focal Adhesion Kinase determine domain-motif interaction affinity and specificity." Biochimica et Biophysica Acta (BBA) - General Subjects 1864, no. 1 (January 2020): 129450. http://dx.doi.org/10.1016/j.bbagen.2019.129450.
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Lu, Zhisheng, Julien R. C. Bergeron, R. Andrew Atkinson, Torsten Schaller, Dennis A. Veselkov, Alain Oregioni, Yi Yang, Stephen J. Matthews, Michael H. Malim, and Mark R. Sanderson. "Insight into the HIV-1 Vif SOCS-box–ElonginBC interaction." Open Biology 3, no. 11 (November 2013): 130100. http://dx.doi.org/10.1098/rsob.130100.
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The HIV-1 viral infectivity factor (Vif) neutralizes cell-encoded antiviral APOBEC3 proteins by recruiting a cellular ElonginB (EloB)/ElonginC (EloC)/Cullin5-containing ubiquitin ligase complex, resulting in APOBEC3 ubiquitination and proteolysis. The suppressors-of-cytokine-signalling-like domain (SOCS-box) of HIV-1 Vif is essential for E3 ligase engagement, and contains a BC box as well as an unusual proline-rich motif. Here, we report the NMR solution structure of the Vif SOCS–ElonginBC (EloBC) complex. In contrast to SOCS-boxes described in other proteins, the HIV-1 Vif SOCS-box contains only one α-helical domain followed by a β-sheet fold. The SOCS-box of Vif binds primarily to EloC by hydrophobic interactions. The functionally essential proline-rich motif mediates a direct but weak interaction with residues 101–104 of EloB, inducing a conformational change from an unstructured state to a structured state. The structure of the complex and biophysical studies provide detailed insight into the function of Vif's proline-rich motif and reveal novel dynamic information on the Vif–EloBC interaction.
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Barletta, Frank, Chi-Wai Wong, Chris McNally, Barry S. Komm, Benita Katzenellenbogen, and Boris J. Cheskis. "Characterization of the Interactions of Estrogen Receptor and MNAR in the Activation of cSrc." Molecular Endocrinology 18, no. 5 (May 1, 2004): 1096–108. http://dx.doi.org/10.1210/me.2003-0335.
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Abstract In this study, we have evaluated the molecular mechanism of Src activation after its interaction with estrogen receptor α (ERα) and a newly identified scaffold protein, called MNAR (modulator of nongenomic activity of ER). Under basal condition, Src enzymatic activity is inhibited by intramolecular interactions. The enzyme can be activated by interaction between the SH2 domain of Src and phosphotyrosine-containing sequences and/or by interaction between the SH3 domain of Src and proteins containing PXXP motifs. Mutational analysis and functional evaluation of MNAR and the use of ERα and cSrc mutants revealed that MNAR interacts with Src’s SH3 domain via its N-terminal PXXP motif. Mutation of this motif abolished both the MNAR-induced activation of Src and the stimulation of ER transcriptional activity. ER interacts with Src’s SH2 domain using phosphotyrosine 537, and this complex was further stabilized by MNAR-ER interaction. Mapping studies reveal that both the A/B domain and Y537 of ERα are required for MNAR-induced activation of ER transcriptional activity. The region responsible for MNAR interaction with ER maps to two N-terminal LXXLL motifs of MNAR. Mutation of these motifs prevented ER-MNAR complex formation and eliminated activation of the Src/MAPK pathway. These data explicate how the coordinate interactions between MNAR, ER, and Src lead to Src activation. Our findings also demonstrate that MNAR is a scaffold protein that mediates ER-Src interaction and plays an important role in the integration of ER action in Src-mediated signaling.
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Cao, T., K. L. Borden, P. S. Freemont, and L. D. Etkin. "Involvement of the rfp tripartite motif in protein-protein interactions and subcellular distribution." Journal of Cell Science 110, no. 14 (July 15, 1997): 1563–71. http://dx.doi.org/10.1242/jcs.110.14.1563.
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The ret finger protein (rfp) is a member of the B box zinc finger gene family which possesses a tripartite motif consisting of a RING finger, B box finger, and a coiled-coil domain. Rfp is expressed at specific stages of spermatogenesis and in various adult mouse and human tissues. It becomes oncogenic when the tripartite domain is recombined with the tyrosine kinase domain of the ret protooncogene. Many of the B box family proteins function as homodimers, although the role of the individual components of the tripartite motif in this process remains unclear. We demonstrate that rfp homomultimerization occurs through the coiled-coil domains; however, while the B box is not an interacting interface itself, its structural integrity is necessary for this interaction to occur. This is the first evidence that the B box zinc finger domain is involved in regulating protein-protein interactions. Interestingly, we find that mutations of the RING finger and B box affect the subcellular compartmentalization of rfp in various cell lines. These results demonstrate that the interactions of rfp with itself and its association with specific subcellular compartments is dependent upon the function of all of the components of the tripartite motif. It is likely that these domains play a crucial role in the function of the rfp protein in normal cell differentiation and in its transformation potential in the recombined state.
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Bayly, Richard, Takayuki Murase, Brandy D. Hyndman, Rachel Savage, Salima Nurmohamed, Kim Munro, Richard Casselman, Steven P. Smith, and David P. LeBrun. "Critical Role for a Single Leucine Residue in Leukemia Induction by E2A-PBX1." Molecular and Cellular Biology 26, no. 17 (September 1, 2006): 6442–52. http://dx.doi.org/10.1128/mcb.02025-05.
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ABSTRACT In roughly 5% of cases of acute lymphoblastic leukemia, a chromosomal translocation leads to expression of the oncogenic protein E2A-PBX1. The N-terminal portion of E2A-PBX1, encoded by the E2A gene, is identical in sequence to the corresponding portion of the E proteins E12/E47 and includes transcriptional activation domains. The C terminus consists of most of the HOX interacting transcription factor PBX1, including its DNA-binding homeodomain. Structure-function correlative experiments have suggested that oncogenesis by E2A-PBX1 requires an activation domain, called AD1, at the extreme N terminus. We recently demonstrated that a potentially helical portion of AD1 interacts directly with the transcriptional coactivator protein cyclic AMP response element-binding protein (CBP) and that this interaction is essential in the immortalization of primary bone marrow cells in tissue culture. Here we show that a conserved LXXLL motif within AD1 is required in the interaction between E2A-PBX1 and the KIX domain of CBP. We show by circular dichroism spectroscopy that the LXXLL-containing portion of AD1 undergoes a helical transition upon interacting with the KIX domain and that amino acid substitutions that prevent helix formation prevent both the KIX interaction and cell immortalization by E2A-PBX1. Perhaps most strikingly, substitution of a single, conserved leucine residue (L20) within the LXXLL motif impairs leukemia induction in mice after transplantation with E2A-PBX1-expressing bone marrow. The KIX domain of CBP mediates well-characterized interactions with several transcription factors of relevance to leukemia induction. Circumstantial evidence suggests that the side chain of L20 might interact with a deep hydrophobic pocket in the KIX domain. Therefore, our results serve to identify a potential new drug target.
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Guerra-Peraza, Orlene, Marc de Tapia, Thomas Hohn, and Maja Hemmings-Mieszczak. "Interaction of the Cauliflower Mosaic Virus Coat Protein with the Pregenomic RNA Leader." Journal of Virology 74, no. 5 (March 1, 2000): 2067–72. http://dx.doi.org/10.1128/jvi.74.5.2067-2072.2000.
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ABSTRACT Using the yeast three-hybrid system, the interaction of theCauliflower mosaic virus (CaMV) pregenomic 35S RNA (pgRNA) leader with the viral coat protein, its precursor, and a series of derivatives was studied. The purine-rich domain in the center of the pgRNA leader was found to specifically interact with the coat protein. The zinc finger motif of the coat protein and the preceding basic domain were essential for this interaction. Removal of the N-terminal portion of the basic domain led to loss of specificity but did not affect the strength of the interaction. Mutations of the zinc finger motif abolished not only the interaction with the RNA but also viral infectivity. In the presence of the very acidic C-terminal domain, which is part of the preprotein but is not present in the mature CP, the interaction with the RNA was undetectable.
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Denis, Christopher M., Seth Chitayat, Michael J. Plevin, Feng Wang, Patrick Thompson, Shuang Liu, Holly L. Spencer, Mitsuhiko Ikura, David P. LeBrun, and Steven P. Smith. "Structural basis of CBP/p300 recruitment in leukemia induction by E2A-PBX1." Blood 120, no. 19 (November 8, 2012): 3968–77. http://dx.doi.org/10.1182/blood-2012-02-411397.
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Abstract E-proteins are critical transcription factors in B-cell lymphopoiesis. E2A, 1 of 3 E-protein–encoding genes, is implicated in the induction of acute lymphoblastic leukemia through its involvement in the chromosomal translocation 1;19 and consequent expression of the E2A-PBX1 oncoprotein. An interaction involving a region within the N-terminal transcriptional activation domain of E2A-PBX1, termed the PCET motif, which has previously been implicated in E-protein silencing, and the KIX domain of the transcriptional coactivator CBP/p300, critical for leukemogenesis. However, the structural details of this interaction remain unknown. Here we report the structure of a 1:1 complex between PCET motif peptide and the KIX domain. Residues throughout the helical PCET motif that contact the KIX domain are important for both binding KIX and bone marrow immortalization by E2A-PBX1. These results provide molecular insights into E-protein–driven differentiation of B-cells and the mechanism of E-protein silencing, and reveal the PCET/KIX interaction as a therapeutic target for E2A-PBX1–induced leukemia.
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Chavakis, Triantafyllos, Valeria Orlova, Kaimei Song, Cornelia L. Andrei-Selmer, and Sentot Santoso. "Heterophilic and Homophilic Interactions of Junctional Adhesion Molecule-C (JAM-C) Mediate Different Intercellular Adhesive Interactions." Blood 106, no. 11 (November 16, 2005): 534. http://dx.doi.org/10.1182/blood.v106.11.534.534.
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Abstract Junctional adhesion molecules (JAM) are a new subfamily of the Ig superfamily. We recently identified that the third member of this family, JAM-C, expressed on endothelial, epithelial cells and platelets (i) undergoes a heterophilic interaction with leukocyte β2-integrin Mac-1 (CD11b/CD18) (J Exp Med. 2002; 196:679–91) and (ii) that endothelial JAM-C is predominantly localized within tight junctions and mediates neutrophil transendothelial migration in a Mac-1-dependent manner in vitro and in vivo (J Biol Chem. 2004, 279:55602–8). Here, we characterized JAM-C to undergo a homophilic interaction that participates in tumor cell-endothelial cell interactions. As assessed in a purified system, recombinant soluble JAM-C in fluid phase bound to immobilized JAM-C; moreover, JAM-C-transfected CHO cells adhered to immobilized JAM-C. The homophilic interaction of JAM-C was mediated by the isolated amino-terminal Ig-domain (D1) but not the carboxy-terminal Ig-domain (D2) of the molecule. Dimerization of JAM-A is dependent on the sequence RVE in the aminoterminal Ig-domain. This motif is conserved in JAM-C (R64I65E66) and a single amino acid mutation in this motif (E66R) abolished the homophilic interaction of JAM-C. The lung carcinoma cell line NCI-H522 was found to be positive for JAM-C expression. NCI-H522 cells adhered to immobilized JAM-C, as well as to JAM-C-transfected CHO cells, but not to mock-transfected CHO cells or to CHO cells transfected with the JAM-C mutant (E66R). Adhesion of NCI-H522 cells to JAM-C protein or JAM-C-transfected CHO cells was abolished in the presence of soluble JAM-C or the isolated D1. Furthermore, the adhesion of NCI-H522 cells to endothelial cells was significantly blocked by soluble JAM-C or the isolated D1. Thus, JAM-C undergoes a homophilic interaction via the R64I65E66 motif on the membrane-distal Ig-domain of the molecule. The homophilic interaction of JAM-C can mediate tumor cell-endothelial cell interactions and may thereby be involved in the process of tumor cell metastasis. Together, the heterophilic and homophilic interactions of JAM-C mediate distinct adhesive interactions.
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Mansour, Hala, Alejandro Cabezas-Cruz, Véronique Peucelle, Amaury Farce, Sophie Salomé-Desnoulez, Ines Metatla, Ida Chiara Guerrera, Thomas Hollin, and Jamal Khalife. "Characterization of GEXP15 as a Potential Regulator of Protein Phosphatase 1 in Plasmodium falciparum." International Journal of Molecular Sciences 24, no. 16 (August 10, 2023): 12647. http://dx.doi.org/10.3390/ijms241612647.
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The Protein Phosphatase type 1 catalytic subunit (PP1c) (PF3D7_1414400) operates in combination with various regulatory proteins to specifically direct and control its phosphatase activity. However, there is little information about this phosphatase and its regulators in the human malaria parasite, Plasmodium falciparum. To address this knowledge gap, we conducted a comprehensive investigation into the structural and functional characteristics of a conserved Plasmodium-specific regulator called Gametocyte EXported Protein 15, GEXP15 (PF3D7_1031600). Through in silico analysis, we identified three significant regions of interest in GEXP15: an N-terminal region housing a PP1-interacting RVxF motif, a conserved domain whose function is unknown, and a GYF-like domain that potentially facilitates specific protein–protein interactions. To further elucidate the role of GEXP15, we conducted in vitro interaction studies that demonstrated a direct interaction between GEXP15 and PP1 via the RVxF-binding motif. This interaction was found to enhance the phosphatase activity of PP1. Additionally, utilizing a transgenic GEXP15-tagged line and live microscopy, we observed high expression of GEXP15 in late asexual stages of the parasite, with localization predominantly in the nucleus. Immunoprecipitation assays followed by mass spectrometry analyses revealed the interaction of GEXP15 with ribosomal- and RNA-binding proteins. Furthermore, through pull-down analyses of recombinant functional domains of His-tagged GEXP15, we confirmed its binding to the ribosomal complex via the GYF domain. Collectively, our study sheds light on the PfGEXP15–PP1–ribosome interaction, which plays a crucial role in protein translation. These findings suggest that PfGEXP15 could serve as a potential target for the development of malaria drugs.
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Das, Chinmaya Kumar, Umasankar Nayak, Preetinanda Pati, Mihir Ranjan Mohanty, Sujata Das, Parshuram Sial, Bhagban Kabat, and S. C. Swain. "Deciphering the Molecular Architecture of a Candidate R-gene (BjuWRR1) Product Mediating White Rust Resistance in Brassica juncea." International Journal of Bio-resource and Stress Management 12, no. 5 (August 31, 2021): 393–401. http://dx.doi.org/10.23910/1.2021.2205a.
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In this investigation, a three-dimensional model of a R-gene encoded product BjuWRR1 which is known to play a role in white rust resistance in Brassica juncea was developed to synthesize innovative ways for evolving white rust resistant cultivars. The model was built from the amino acid sequence of BjuWRR1 using structural template information of a disease resistance protein (RPP13-like protein 4 of Arabidopsis thaliana) with the help of homology-based modelling approach. Built models were validated for their stereochemical parameters and structural descriptors using Ramachandran plot analysis, protein structure analysis and ERRAT analysis. Structural analysis of BjuWRR1 model revealed that it is composed of three distinct domains namely a coiled-coil domain, a central NB-ARC nucleotide binding domain and a hypervariable leucine-rich repeat domain. Further, canonical conserved motifs such as P-loop, Kinase2-motif and HD-motif were found in the NB-ARC domain. The built model would help in understanding the molecular basis of plant-immunity against white rust pathogen by understanding the significance of inter-domain interactions in BuWRR1 in triggering the activation of downstream defense response against the white rust pathogen by promoting oligomerization of coiled-coil domains through stabilized hydrophobic interactions and interaction with NB-ARC domain. Presence of patches of charged residues in each domain of BjuWRR1 indicated their possible role in intra-molecular interaction with other domains. Therefore, this model can help in designing functional genomic studies to understand the role of intra-molecular interaction in BjuWRR1 to mediate resistance against white rust pathogen.
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Batzer, A. G., P. Blaikie, K. Nelson, J. Schlessinger, and B. Margolis. "The phosphotyrosine interaction domain of Shc binds an LXNPXY motif on the epidermal growth factor receptor." Molecular and Cellular Biology 15, no. 8 (August 1995): 4403–9. http://dx.doi.org/10.1128/mcb.15.8.4403.
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Shc is an SH2 domain protein that is tyrosine phosphorylated in cells stimulated with a variety of growth factors and cytokines. Once phosphorylated, Shc binds the Grb2-Sos complex, leading to Ras activation. Shc can interact with tyrosine-phosphorylated proteins by binding to phosphotyrosine in the context of an NPXpY motif, where pY is a phosphotyrosine. This is an unusual binding site for an SH2 domain protein whose binding specificity is usually controlled by residues carboxy terminal, not amino terminal, to the phosphotyrosine. Recently we identified a second region in Shc, named the phosphotyrosine interaction (PI) domain, and we have found it to be present in a variety of other cellular proteins. In this study we used a dephosphorylation protection assay, competition analysis with phosphotyrosine-containing synthetic peptides, and epidermal growth factor receptor (EGFR) mutants to determine the binding sites of the PI domain of Shc on the EGFR. We demonstrate that the PI domain of Shc binds the LXNPXpY motif that encompasses Y-1148 of the activated EGFR. We conclude that the PI domain imparts to Shc its ability to bind the NPXpY motif.
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Hodge, Kenneth, Chairat Tunghirun, Maliwan Kamkaew, Thawornchai Limjindaporn, Pa-thai Yenchitsomanus, and Sarin Chimnaronk. "Identification of a Conserved RNA-dependent RNA Polymerase (RdRp)-RNA Interface Required for Flaviviral Replication." Journal of Biological Chemistry 291, no. 33 (June 22, 2016): 17437–49. http://dx.doi.org/10.1074/jbc.m116.724013.
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Dengue virus, an ∼10.7-kb positive-sense RNA virus, is the most common arthropod-communicated pathogen in the world. Despite dengue's clear epidemiological importance, mechanisms for its replication remain elusive. Here, we probed the entire dengue genome for interactions with viral RNA-dependent RNA polymerase (RdRp), and we identified the dominant interaction as a loop-forming ACAG motif in the 3′ positive-stranded terminus, complicating the prevailing model of replication. A subset of interactions coincides with known flaviviral recombination sites inside the viral protein-coding region. Specific recognition of the RNA element occurs via an arginine patch in the C-terminal thumb domain of RdRp. We also show that the highly conserved nature of the consensus RNA motif may relate to its tolerance to various mutations in the interacting region of RdRp. Disruption of the interaction resulted in loss of viral replication ability in cells. This unique RdRp-RNA interface is found throughout flaviviruses, implying possibilities for broad disease interventions.
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Kim, I. S., S. Sinha, B. de Crombrugghe, and S. N. Maity. "Determination of functional domains in the C subunit of the CCAAT-binding factor (CBF) necessary for formation of a CBF-DNA complex: CBF-B interacts simultaneously with both the CBF-A and CBF-C subunits to form a heterotrimeric CBF molecule." Molecular and Cellular Biology 16, no. 8 (August 1996): 4003–13. http://dx.doi.org/10.1128/mcb.16.8.4003.
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The mammalian CCAAT-binding factor (CBF; also called NF-Y and CP1) is a heterotrimeric protein consisting of three subunits, CBF-A, CBF-B, and CBF-C, all of which are required for DNA binding and all of which are present in the CBF-DNA complex. In this study using cross-linking and immunoprecipitation methods, we first established that CBF-B interacts simultaneously with both subunits of the CBF-A-CBF-C heterodimer to form a heterotrimeric CBF molecule. We then performed a mutational analysis of CBF-C to define functional interactions with the other two CBF subunits and with DNA using several in vitro assays and an in vivo yeast two-hybrid system. Our experiments established that the evolutionarily conserved segment of CBF-C, which shows similarities with the histone-fold motif of histone H2A, was necessary for formation of the CBF-DNA complex. The domain of CBF-C which interacts with CBF-A included a large portion of this segment, one that corresponds to the segment of the histone-fold motif in H2A used for interaction with H2B. Two classes of interactions involved in formation of the CBF-A-CBF-C heterodimer were detected; one class, provided by residues in the middle of the interaction domain, was needed for formation of the CBF-A-CBF-C heterodimer. The other, provided by sequences flanking those of the first class was needed for stabilization of the heterodimer. Two separate domains were identified in the conserved segment of CBF-C for interaction with CBF-B; these were located on each side of the CBF-A interaction domain. Since our previous experiments identified a single CBF-B interaction domain in the histone-fold motif of CBF-A, we propose that a tridentate interaction domain in the CBF-A-CBF-C heterodimer interacts with the 21-amino-acid-long subunit interaction domain of CBF-B. Together with our previous mutational analysis of CBF-A (S. Sinha, I.-S. Kim, K.-Y. Sohn, B. de Crombrugghe, and S. N. Maity, Mol. Cell. Biol. 16:328-337, 1996), this study demonstrates that the histone fold-motifs of CBF-A and CBF-C interact with each other to form the CBF-A-CBF-C heterodimer and generate a hybrid surface which then interacts with CBF-B to form the heterotrimeric CBF molecule.
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Kobor, Michael S., Lisa D. Simon, Jim Omichinski, Guoqing Zhong, Jacques Archambault, and Jack Greenblatt. "A Motif Shared by TFIIF and TFIIB Mediates Their Interaction with the RNA Polymerase II Carboxy-Terminal Domain Phosphatase Fcp1p in Saccharomyces cerevisiae." Molecular and Cellular Biology 20, no. 20 (October 15, 2000): 7438–49. http://dx.doi.org/10.1128/mcb.20.20.7438-7449.2000.
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ABSTRACT Transcription by RNA polymerase II is accompanied by cyclic phosphorylation and dephosphorylation of the carboxy-terminal heptapeptide repeat domain (CTD) of its largest subunit. We have used deletion and point mutations in Fcp1p, a TFIIF-interacting CTD phosphatase, to show that the integrity of its BRCT domain, like that of its catalytic domain, is important for cell viability, mRNA synthesis, and CTD dephosphorylation in vivo. Although regions of Fcp1p carboxy terminal to its BRCT domain and at its amino terminus were not essential for viability, deletion of either of these regions affected the phosphorylation state of the CTD. Two portions of this carboxy-terminal region of Fcp1p bound directly to the first cyclin-like repeat in the core domain of the general transcription factor TFIIB, as well as to the RAP74 subunit of TFIIF. These regulatory interactions with Fcp1p involved closely related amino acid sequence motifs in TFIIB and RAP74. Mutating the Fcp1p-binding motif KEFGK in the RAP74 (Tfg1p) subunit of TFIIF to EEFGE led to both synthetic phenotypes in certain fcp1 tfg1 double mutants and a reduced ability of Fcp1p to activate transcription when it is artificially tethered to a promoter. These results suggest strongly that this KEFGK motif in RAP74 mediates its interaction with Fcp1p in vivo.
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Ala-Poikela, Marjo, Minna-Liisa Rajamäki, and Jari P. T. Valkonen. "A Novel Interaction Network Used by Potyviruses in Virus–Host Interactions at the Protein Level." Viruses 11, no. 12 (December 14, 2019): 1158. http://dx.doi.org/10.3390/v11121158.
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Host proteins that are central to infection of potyviruses (genus Potyvirus; family Potyviridae) include the eukaryotic translation initiation factors eIF4E and eIF(iso)4E. The potyviral genome-linked protein (VPg) and the helper component proteinase (HCpro) interact with each other and with eIF4E and eIF(iso)4E and proteins are involved in the same functions during viral infection. VPg interacts with eIF4E/eIF(iso)4E via the 7-methylguanosine cap-binding region, whereas HCpro interacts with eIF4E/eIF(iso)4E via the 4E-binding motif YXXXXLΦ, similar to the motif in eIF4G. In this study, HCpro and VPg were found to interact in the nucleus, nucleolus, and cytoplasm in cells infected with the potyvirus potato virus A (PVA). In the cytoplasm, interactions between HCpro and VPg occurred in punctate bodies not associated with viral replication vesicles. In addition to HCpro, the 4E-binding motif was recognized in VPg of PVA. Mutations in the 4E-binding motif of VPg from PVA weakened interactions with eIF4E and heavily reduced PVA virulence. Furthermore, mutations in the 4G-binding domain of eIF4E reduced interactions with VPg and abolished interactions with HCpro. Thus, HCpro and VPg can both interact with eIF4E using the 4E-binding motif. Our results suggest a novel interaction network used by potyviruses to interact with host plants via translation initiation factors.
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Songyang, Zhou, Benjamin Margolis, Manas Chaudhuri, Steve E. Shoelson, and Lewis C. Cantley. "The Phosphotyrosine Interaction Domain of SHC Recognizes Tyrosine-phosphorylated NPXY Motif." Journal of Biological Chemistry 270, no. 25 (June 23, 1995): 14863–66. http://dx.doi.org/10.1074/jbc.270.25.14863.
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Wu, Nan-Ying, and Soo-Chen Cheng. "Functional analysis of Cwc24 ZF-domain in 5′ splice site selection." Nucleic Acids Research 47, no. 19 (August 28, 2019): 10327–39. http://dx.doi.org/10.1093/nar/gkz733.
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Abstract The essential splicing factor Cwc24 contains a zinc-finger (ZF) domain required for its function in splicing. Cwc24 binds over the 5′ splice site after the spliceosome is activated, and its binding prior to Prp2-mediated spliceosome remodeling is important for proper interactions of U5 and U6 with the 5′ splice site sequence and selection of the 5′ splice site. Here, we show that Cwc24 transiently interacts with the 5′ splice site in formation of the functional RNA catalytic core during spliceosome remodeling, and the ZF-motif is required for specific interaction of Cwc24 with the 5′ splice site. Deletion of the ZF domain or mutation of the conserved ZF residues greatly weakened the association of Cwc24 with the spliceosome, and lowered the affinity and specificity of its interaction with the 5′ splice site, resulting in atypical interactions of U5, U6 and Prp8 with the 5′ splice site, and aberrant cleavage at the 5′ splice site. Our results reveal a crucial role of the Cwc24 ZF-motif for defining 5′ splice site selection in the first splicing step.
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van de Wijngaart, Dennis J., Hendrikus J. Dubbink, Michel Molier, Carola de Vos, Jan Trapman, and Guido Jenster. "Functional Screening of FxxLF-Like Peptide Motifs Identifies SMARCD1/BAF60a as an Androgen Receptor Cofactor that Modulates TMPRSS2 Expression." Molecular Endocrinology 23, no. 11 (November 1, 2009): 1776–86. http://dx.doi.org/10.1210/me.2008-0280.
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Abstract Androgen receptor (AR) transcriptional activity is tightly regulated by interacting cofactors and cofactor complexes. The best described cofactor interaction site in the AR is the hormone-induced coactivator binding groove in the ligand-binding domain, which serves as a high-affinity docking site for FxxLF-like motifs. This study aimed at identifying novel AR cofactors by in silico selection and functional screening of FxxLF-like peptide motifs. Candidate interacting motifs were selected from a proteome-wide screening and from a supervised screening focusing on components of protein complexes involved in transcriptional regulation. Of the 104 peptides tested, 12 displayed moderate to strong in vivo hormone-dependent interactions with AR. For three of these, ZBTB16/PLZF, SMARCA4/BRG1, and SMARCD1/BAF60a, the full-length protein was tested for interaction with AR. Of these, BAF60a, a subunit of the SWI/SNF chromatin remodeling complex, displayed hormone-dependent interactions with AR through its FxxFF motif. Vice versa, recruitment of BAF60a by the AR required an intact coactivator groove. BAF60a depletion by small interfering RNA in LNCaP cells demonstrated differential effects on expression of endogenous AR target genes. AR-driven expression of TMPRSS2 was almost completely blocked by BAF60a small interfering RNA. In summary, our data demonstrate that BAF60a directly interacts with the coactivator groove in the AR ligand-binding domain via its FxxFF motif, thereby selectively activating specific AR-driven promoters.
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Kang, Jee Eun, Ji Hae Jun, Jung Hyun Kwon, Ju-Hyun Lee, Kidong Hwang, Sungjong Kim, and Namhee Jeong. "Arabidopsis Transcription Regulatory Factor Domain/Domain Interaction Analysis Tool—Liquid/Liquid Phase Separation, Oligomerization, GO Analysis: A Toolkit for Interaction Data-Based Domain Analysis." Genes 14, no. 7 (July 19, 2023): 1476. http://dx.doi.org/10.3390/genes14071476.
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Although a large number of databases are available for regulatory elements, a bottleneck has been created by the lack of bioinformatics tools to predict the interaction modes of regulatory elements. To reduce this gap, we developed the Arabidopsis Transcription Regulatory Factor Domain/Domain Interaction Analysis Tool–liquid/liquid phase separation (LLPS), oligomerization, GO analysis (ART FOUNDATION-LOG), a useful toolkit for protein–nucleic acid interaction (PNI) and protein–protein interaction (PPI) analysis based on domain–domain interactions (DDIs). LLPS, protein oligomerization, the structural properties of protein domains, and protein modifications are major components in the orchestration of the spatiotemporal dynamics of PPIs and PNIs. Our goal is to integrate PPI/PNI information into the development of a prediction model for identifying important genetic variants in peaches. Our program unified interdatabase relational keys based on protein domains to facilitate inference from the model species. A key advantage of this program lies in the integrated information of related features, such as protein oligomerization, LOG analysis, structural characterizations of domains (e.g., domain linkers, intrinsically disordered regions, DDIs, domain–motif (peptide) interactions, beta sheets, and transmembrane helices), and post-translational modification. We provided simple tests to demonstrate how to use this program, which can be applied to other eukaryotic organisms.
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Chu, Anh, Yeqi Yao, Miroslawa Glibowicka, Charles M. Deber, and Morris F. Manolson. "The Human Mutation K237_V238del in a Putative Lipid Binding Motif within the V-ATPase a2 Isoform Suggests a Molecular Mechanism Underlying Cutis Laxa." International Journal of Molecular Sciences 25, no. 4 (February 11, 2024): 2170. http://dx.doi.org/10.3390/ijms25042170.
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Vacuolar ATPases (V-ATPases), proton pumps composed of 16 subunits, are necessary for a variety of cellular functions. Subunit “a” has four isoforms, a1–a4, each with a distinct cellular location. We identified a phosphoinositide (PIP) interaction motif, KXnK(R)IK(R), conserved in all four isoforms, and hypothesize that a/PIP interactions regulate V-ATPase recruitment/retention to different organelles. Among the four isoforms, a2 is enriched on Golgi with a2 mutations in the PIP motif resulting in cutis laxa. We hypothesize that the hydrophilic N-terminal (NT) domain of a2 contains a lipid-binding domain, and mutations in this domain prevent interaction with Golgi-enriched PIPs, resulting in cutis laxa. We recreated the cutis laxa-causing mutation K237_V238del, and a double mutation in the PIP-binding motif, K237A/V238A. Circular dichroism confirmed that there were no protein structure alterations. Pull-down assays with PIP-enriched liposomes revealed that wildtype a2NT preferentially binds phosphatidylinositol 4-phosphate (PI(4)P), while mutants decreased binding to PI(4)P. In HEK293 cells, wildtype a2NT was localized to Golgi and co-purified with microsomal membranes. Mutants reduced Golgi localization and membrane association. Rapamycin depletion of PI(4)P diminished a2NT-Golgi localization. We conclude that a2NT is sufficient for Golgi retention, suggesting the lipid-binding motif is involved in V-ATPase targeting and/or retention. Mutational analyses suggest a molecular mechanism underlying how a2 mutations result in cutis laxa.
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Kwok, Ethiene, Diego J. Rodriguez, Joachim Kremerskothen, and Afua Nyarko. "Intrinsic disorder and amino acid specificity modulate binding of the WW2 domain in kidney and brain protein (KIBRA) to synaptopodin." Journal of Biological Chemistry 294, no. 46 (October 9, 2019): 17383–94. http://dx.doi.org/10.1074/jbc.ra119.009589.
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The second WW domain (WW2) of the kidney and brain scaffolding protein, KIBRA, has an isoleucine (Ile-81) rather than a second conserved tryptophan and is primarily unstructured. However, it adopts the canonical triple-stranded antiparallel β-sheet structure of WW domains when bound to a two-PPXY motif peptide of the synaptic protein Dendrin. Here, using a series of biophysical experiments, we demonstrate that the WW2 domain remains largely disordered when bound to a 69-residue two-PPXY motif polypeptide of the synaptic and podocyte protein synaptopodin (SYNPO). Isothermal titration calorimetry and CD experiments revealed that the interactions of the disordered WW2 domain with SYNPO are significantly weaker than SYNPO's interactions with the well-folded WW1 domain and that an I81W substitution in the WW2 domain neither enhances binding affinity nor induces substantial WW2 domain folding. In the tandem polypeptide, the two WW domains synergized, enhancing the overall binding affinity with the I81W variant tandem polypeptide 2-fold compared with the WT polypeptide. Solution NMR results showed that SYNPO binding induces small but definite chemical shift perturbations in the WW2 domain, confirming the disordered state of the WW2 domain in this complex. These analyses also disclosed that SYNPO binds the tandem WW domain polypeptide in an antiparallel manner, that is, the WW1 domain binds the second PPXY motif of SYNPO. We propose a binding model consisting of a bipartite interaction mode in which the largely disordered WW2 forms a “fuzzy” complex with SYNPO. This binding mode may be important for specific cellular functions.
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Chen, Zhuoyao, Jinwei Zhang, Adrián R. Murillo-de-Ozores, María Castañeda-Bueno, Francesca D'Amico, Raphael Heilig, Charlotte E. Manning, et al. "Sequence and structural variations determining the recruitment of WNK kinases to the KLHL3 E3 ligase." Biochemical Journal 479, no. 5 (March 4, 2022): 661–75. http://dx.doi.org/10.1042/bcj20220019.
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The BTB-Kelch protein KLHL3 is a Cullin3-dependent E3 ligase that mediates the ubiquitin-dependent degradation of kinases WNK1–4 to control blood pressure and cell volume. A crystal structure of KLHL3 has defined its binding to an acidic degron motif containing a PXXP sequence that is strictly conserved in WNK1, WNK2 and WNK4. Mutations in the second proline abrograte the interaction causing the hypertension syndrome pseudohypoaldosteronism type II. WNK3 shows a diverged degron motif containing four amino acid substitutions that remove the PXXP motif raising questions as to the mechanism of its binding. To understand this atypical interaction, we determined the crystal structure of the KLHL3 Kelch domain in complex with a WNK3 peptide. The electron density enabled the complete 11-mer WNK-family degron motif to be traced for the first time revealing several conserved features not captured in previous work, including additional salt bridge and hydrogen bond interactions. Overall, the WNK3 peptide adopted a conserved binding pose except for a subtle shift to accommodate bulkier amino acid substitutions at the binding interface. At the centre, the second proline was substituted by WNK3 Thr541, providing a unique phosphorylatable residue among the WNK-family degrons. Fluorescence polarisation and structural modelling experiments revealed that its phosphorylation would abrogate the KLHL3 interaction similarly to hypertension-causing mutations. Together, these data reveal how the KLHL3 Kelch domain can accommodate the binding of multiple WNK isoforms and highlight a potential regulatory mechanism for the recruitment of WNK3.
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Rovnak, Joel, and Sandra L. Quackenbush. "Walleye Dermal Sarcoma Virus Retroviral Cyclin Directly Contacts TAF9." Journal of Virology 80, no. 24 (October 11, 2006): 12041–48. http://dx.doi.org/10.1128/jvi.01425-06.
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ABSTRACT Walleye dermal sarcoma virus (WDSV) is a complex retrovirus associated with dermal sarcomas in walleye fish. A WDSV accessory gene encodes a cyclin homolog or retroviral cyclin (rv-cyclin). WDSV rv-cyclin was found to be associated with transcription complexes and to affect transcription in a cell-type and promoter-dependent manner. It inhibited the WDSV promoter in walleye fibroblasts and activated transcription from GAL4 promoters when fused to the GAL4 DNA binding domain, and an activation domain (AD) has been localized to 30 amino acids in the carboxyl region. rv-cyclin can block the pulldown of transcription coactivators by the AD of VP16, and the isolated rv-cyclin AD interferes specifically with the interaction between the carboxyl halves of the VP16 AD, VP16C, and TATA-binding protein-associated factor 9 (TAF9). The carboxyl region and isolated AD can bind TAF9 directly in assays of protein-protein interaction in vitro. Furthermore, rv-cyclin and the isolated rv-cyclin AD interfere specifically with the function of VP16C in transcription assays. A previously identified motif within the VP16C sequence mediates TAF9 binding, and this motif is present in the activation domains of a variety of TAF9-binding transcriptional activators. A similar motif is present in the rv-cyclin AD, and point mutations within this motif affect rv-cyclin function and protein-protein interactions. The results support a model of transcription regulation by direct interaction with TAF9.
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Huang, Qingling, Lihong Chen, Leixiang Yang, Xiaoling Xie, Lin Gan, John L. Cleveland, and Jiandong Chen. "MDMX acidic domain inhibits p53 DNA binding in vivo and regulates tumorigenesis." Proceedings of the National Academy of Sciences 115, no. 15 (March 26, 2018): E3368—E3377. http://dx.doi.org/10.1073/pnas.1719090115.
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The MDM2 homolog MDMX oncoprotein is indispensable for inhibition of p53 during normal embryonic development and malignant transformation, yet how MDMX harnesses p53 functions is unclear. In addition to a canonical N-terminal p53-binding domain, recent work suggests the central acidic domain of MDMX regulates p53 interaction through intramolecular mimicry and engages in second-site interaction with the p53 core domain in vitro. To test the physiological relevance of these interactions, we generated an MDMX knockin mouse having substitutions in a conserved WW motif necessary for these functions (W201S/W202G). Notably, MDMXSG cells have normal p53 level but increased p53 DNA binding and target gene expression, and rapidly senesce. In vivo, MDMXSG inhibits early-phase disease in Eµ-Myc transgenic mice but accelerates the onset of lethal lymphoma and shortens overall survival. Therefore, MDMX is an important regulator of p53 DNA binding, which complements the role of MDM2 in regulating p53 level. Furthermore, the results suggest that the WW motif has dual functions that regulate p53 and inhibit Myc-driven lymphomas independent of p53.
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Chai, Zhifang, Daniel A. Goodenough, and David L. Paul. "Cx50 requires an intact PDZ-binding motif and ZO-1 for the formation of functional intercellular channels." Molecular Biology of the Cell 22, no. 23 (December 2011): 4503–12. http://dx.doi.org/10.1091/mbc.e11-05-0438.
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The three connexins expressed in the ocular lens each contain PDZ domain–binding motifs directing a physical association with the scaffolding protein ZO-1, but the significance of the interaction is unknown. We found that Cx50 with PDZ-binding motif mutations did not form gap junction plaques or induce cell–cell communication in HeLa cells, whereas the addition of a seven–amino acid PDZ-binding motif restored normal function to Cx50 lacking its entire C-terminal cytoplasmic domain. C-Terminal deletion had a similar although weaker effect on Cx46 but little if any effect on targeting and function of Cx43. Furthermore, small interfering RNA knockdown of ZO-1 completely inhibited the formation of gap junctions by wild-type Cx50 in HeLa cells. Thus both a PDZ-binding motif and ZO-1 are necessary for Cx50 intercellular channel formation in HeLa cells. Knock-in mice expressing Cx50 with a PDZ-binding motif mutation phenocopied Cx50 knockouts. Furthermore, differentiating lens fibers in the knock-in displayed extensive intracellular Cx50, whereas plaques in mature fibers contained only Cx46. Thus normal Cx50 function in vivo also requires an intact PDZ domain–binding motif. This is the first demonstration of a connexin-specific requirement for a connexin-interacting protein in gap junction assembly.
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Dubbink, Hendrikus J., Remko Hersmus, Ashley C. W. Pike, Michel Molier, Albert O. Brinkmann, Guido Jenster, and Jan Trapman. "Androgen Receptor Ligand-Binding Domain Interaction and Nuclear Receptor Specificity of FXXLF and LXXLL Motifs as Determined by L/F Swapping." Molecular Endocrinology 20, no. 8 (August 1, 2006): 1742–55. http://dx.doi.org/10.1210/me.2005-0348.
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Abstract The androgen receptor (AR) ligand-binding domain (LBD) binds FXXLF motifs, present in the AR N-terminal domain and AR-specific cofactors, and some LXXLL motifs of nuclear receptor coactivators. We demonstrated that in the context of the AR FXXLF motif many different amino acid residues at positions +2 and +3 are compatible with strong AR LBD interaction, although a preference for E at +2 and K or R at +3 was found. Pairwise systematic analysis of F/L swaps at +1 and +5 in FXXLF and LXXLL motifs showed: 1) F to L substitutions in natural FXXLF motifs abolished AR LBD interaction; 2) binding of interacting LXXLL motifs was unchanged or increased upon L to F substitutions; 3) certain noninteracting LXXLL motifs became strongly AR-interacting FXXLF motifs; whereas 4) other nonbinders remained unaffected by L to F substitutions. All FXXLF motifs, but not the corresponding LXXLL motifs, displayed a strong preference for AR LBD. Progesterone receptor LBD interacted with some FXXLF motifs, albeit always less efficiently than corresponding LXXLL motifs. AR LBD interaction of most FXXLF and LXXLL peptides depended on classical charge clamp residue K720, whereas E897 was less important. Other charged residues lining the AR coactivator-binding groove, K717 and R726, modulated optimal peptide binding. Interestingly, these four charged residues affected binding of individual peptides independent of an F or L at +1 and +5 in swap experiments. In conclusion, F residues determine strong and selective peptide interactions with AR. Sequences flanking the core motif determine the specific mode of FXXLF and LXXLL interactions.