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Academic literature on the topic 'Nudix hydrolase proteins'

Author: Grafiati
Published: 6 September 2023

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Journal articles on the topic "Nudix hydrolase proteins"

1

Kraszewska, Elzbieta. "The plant Nudix hydrolase family." Acta Biochimica Polonica 55, no. 4 (December 16, 2008): 663–71. http://dx.doi.org/10.18388/abp.2008_3025.

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Nudix hydrolases are a family of proteins defined by a conserved amino-acid sequence GX(5)-EX(7)REUXEEXGU, where U is a hydrophobic residue. These enzymes are widely distributed among all classes of organisms and catalyze, with varying degrees of substrate specificity, the hydrolysis of a variety of nucleoside diphosphate derivatives: nucleoside di- and triphosphates and their oxidized forms, dinucleoside polyphosphates, nucleotide sugars, NADH, coenzyme A and the mRNA cap. Nudix proteins are postulated to control the cellular concentration of these compounds. The genome of the model plant Arabidopsis thaliana contains 29 genes coding for putative Nudix hydrolases. Recently, several Arabidopsis Nudix genes have been cloned and their products characterized. This review summarizes current knowledge on these plant enzymes and discusses their possible cellular functions.
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2

MAKSEL, Danuta, Paul R. GOOLEY, James D. SWARBRICK, Andrzej GURANOWSKI, Christine GANGE, G. Michael BLACKBURN, and Kenwyn R. GAYLER. "Characterization of active-site residues in diadenosine tetraphosphate hydrolase from Lupinus angustifolius." Biochemical Journal 357, no. 2 (July 9, 2001): 399–405. http://dx.doi.org/10.1042/bj3570399.

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Site-directed mutagenesis has been used to characterize the functions of key amino acid residues in the catalytic site of the ‘nudix’ hydrolase, (asymmetrical) diadenosine 5′,5‴-P1,P4-tetraphosphate (Ap4A) hydrolase (EC 3.6.1.17) from Lupinus angustifolius, the three-dimensional solution structure of which has recently been solved. Residues within the nudix motif, Gly-(Xaa)5-Glu-(Xaa)7-Arg-Glu-Uaa-Xaa-(Glu)2-Xaa-Gly (where Xaa represents unspecified amino acids and Uaa represents the bulky aliphatic amino acids Ile, Leu or Val) conserved in ‘nudix enzymes’, and residues important for catalysis from elsewhere in the molecule, were mutated and the expressed proteins characterized. The results reveal a high degree of functional conservation between lupin asymmetric Ap4A hydrolase and the 8-oxo-dGTP hydrolase from Escherichia coli. Charged residues in positions equivalent to those that ligate an enzyme-bound metal ion in the E. coli 8-oxo-dGTP hydrolase [Harris, Wu, Massiah and Mildvan (2000) Biochemistry 39, 1655–1674] were shown to contribute to catalysis to similar extents in the lupin enzyme. Mutations E55Q, E59Q and E125Q all reduced kcat markedly, whereas mutations R54Q, E58Q and E122Q had smaller effects. None of the mutations produced a substantial change in the Km for Ap4A, but several extensively modified the pH-dependence and fluoride-sensitivities of the hydrolase. It was concluded that the precisely positioned glutamate residues Glu-55, Glu-59 and Glu-125 are conserved as functionally significant components of the hydrolytic mechanism in both of these members of the nudix family of hydrolases.
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3

Karačić, Zrinka, Bojana Vukelić, Gabrielle H. Ho, Iva Jozić, Iva Sučec, Branka Salopek-Sondi, Marija Kozlović, Steven E. Brenner, Jutta Ludwig-Müller, and Marija Abramić. "A novel plant enzyme with dual activity: an atypical Nudix hydrolase and a dipeptidyl peptidase III." Biological Chemistry 398, no. 1 (January 1, 2017): 101–12. http://dx.doi.org/10.1515/hsz-2016-0141.

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Abstract In a search for plant homologues of dipeptidyl peptidase III (DPP III) family, we found a predicted protein from the moss Physcomitrella patens (UniProt entry: A9TLP4), which shared 61% sequence identity with the Arabidopsis thaliana uncharacterized protein, designated Nudix hydrolase 3. Both proteins contained all conserved regions of the DPP III family, but instead of the characteristic hexapeptide HEXXGH zinc-binding motif, they possessed a pentapeptide HEXXH, and at the N-terminus, a Nudix box, a hallmark of Nudix hydrolases, known to act upon a variety of nucleoside diphosphate derivatives. To investigate their biochemical properties, we expressed heterologously and purified Physcomitrella (PpND) and Arabidopsis (AtND) protein. Both hydrolyzed, with comparable catalytic efficiency, the isopentenyl diphosphate (IPP), a universal precursor for the biosynthesis of isoprenoid compounds. In addition, PpND dephosphorylated four purine nucleotides (ADP, dGDP, dGTP, and 8-oxo-dATP) with strong preference for oxidized dATP. Furthermore, PpND and AtND showed DPP III activity against dipeptidyl-2-arylamide substrates, which they cleaved with different specificity. This is the first report of a dual activity enzyme, highly conserved in land plants, which catalyzes the hydrolysis of a peptide bond and of a phosphate bond, acting both as a dipeptidyl peptidase III and an atypical Nudix hydrolase.
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4

Sharma, Sunny, Ewa Grudzien-Nogalska, Keith Hamilton, Xinfu Jiao, Jun Yang, Liang Tong, and Megerditch Kiledjian. "Mammalian Nudix proteins cleave nucleotide metabolite caps on RNAs." Nucleic Acids Research 48, no. 12 (May 20, 2020): 6788–98. http://dx.doi.org/10.1093/nar/gkaa402.

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Abstract We recently reported the presence of nicotinamide adenine dinucleotide (NAD)-capped RNAs in mammalian cells and a role for DXO and the Nudix hydrolase Nudt12 in decapping NAD-capped RNAs (deNADding) in cells. Analysis of 5′caps has revealed that in addition to NAD, mammalian RNAs also contain other metabolite caps including flavin adenine dinucleotide (FAD) and dephosphoCoA (dpCoA). In the present study we systematically screened all mammalian Nudix proteins for their potential deNADing, FAD cap decapping (deFADding) and dpCoA cap decapping (deCoAping) activity. We demonstrate that Nudt16 is a novel deNADding enzyme in mammalian cells. Additionally, we identified seven Nudix proteins—Nudt2, Nudt7, Nudt8, Nudt12, Nudt15, Nudt16 and Nudt19, to possess deCoAping activity in vitro. Moreover, our screening revealed that both mammalian Nudt2 and Nudt16 hydrolyze FAD-capped RNAs in vitro with Nudt16 regulating levels of FAD-capped RNAs in cells. All decapping activities identified hydrolyze the metabolite cap substrate within the diphosphate linkage. Crystal structure of human Nudt16 in complex with FAD at 2.7 Å resolution provide molecular insights into the binding and metal-coordinated hydrolysis of FAD by Nudt16. In summary, our study identifies novel cellular deNADding and deFADding enzymes and establishes a foundation for the selective functionality of the Nudix decapping enzymes on non-canonical metabolite caps.
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5

Parrish, Susan, and Bernard Moss. "Characterization of a Second Vaccinia Virus mRNA-Decapping Enzyme Conserved in Poxviruses." Journal of Virology 81, no. 23 (September 19, 2007): 12973–78. http://dx.doi.org/10.1128/jvi.01668-07.

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ABSTRACT Vaccinia virus (VACV) encodes enzymes that cap the 5′ end of viral mRNAs, which enhances their stability and translation. Nevertheless, recent studies demonstrated that the VACV D10 protein (VACV-WR_115) decaps mRNA, an enzymatic activity not previously shown to be encoded by a virus. The decapping activity of D10 is dependent on a Nudix hydrolase motif that is also present in the VACV D9 protein (VACV-WR_114), which shares 25% sequence identity with D10. Here, we showed that a purified recombinant VACV D9 fusion protein also decaps mRNA and that this activity was abolished by point mutations in the Nudix hydrolase motif. Decapping was specific for a methylated cap attached to RNA and resulted in the liberation of m7GDP. D9 differed from D10 in requiring a longer capped RNA substrate for optimal activity, having greater sensitivity to inhibition by uncapped RNA, and having lower sensitivity to inhibition by nucleotide cap analogs unattached to RNA. Since D9 is expressed early in infection and D10 late, we suggest that the two proteins enhance mRNA turnover and manipulate gene expression in a complementary and overlapping manner.
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6

Tamura, Naoyuki, Yukio Murata, and Takafumi Mukaihara. "Isolation of Ralstonia solanacearum hrpB constitutive mutants and secretion analysis of hrpB-regulated gene products that share homology with known type III effectors and enzymes." Microbiology 151, no. 9 (September 1, 2005): 2873–84. http://dx.doi.org/10.1099/mic.0.28161-0.

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The Hrp type III secretion system (TTSS) is essential for the pathogenicity of the Gram-negative plant pathogen Ralstonia solanacearum. To examine the secretion of type III effector proteins via the Hrp TTSS, a screen was done of mutants constitutively expressing the hrpB gene, which encodes an AraC-type transcriptional activator for the hrp regulon. A mutant was isolated that in an hrp-inducing medium expresses several hrpB-regulated genes 4·9–83-fold higher than the wild-type. R. solanacearum Hrp-secreted outer proteins PopA and PopC were secreted at high levels into the culture supernatants of the hrpB constitutive (hrpB c) mutant. Using hrpB c mutants, the extracellular secretion of several hrpB-regulated (hpx) gene products that share homology with known type III effectors and enzymes was examined. Hpx23, Hpx24 and Hpx25, which are similar in sequence to Pseudomonas syringae pv. tomato effector proteins HopPtoA1, HolPtoR and HopPtoD1, are also secreted via the Hrp TTSS in R. solanacearum. The secretion of two hpx gene products that share homology with known enzymes, glyoxalase I (Hpx19) and Nudix hydrolase (Hpx26), was also examined. Hpx19 is accumulated inside the cell, but interestingly, Hpx26 is secreted outside the cell as an Hrp-secreted outer protein, suggesting that Hpx19 functions intracellularly but Hpx26 is a novel effector protein of R. solanacearum.
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7

Wang, Dan, Qiong Liu, Yan-Long Jiang, Hai-Bin Huang, Jun-Yi Li, Tian-Xu Pan, Nan Wang, et al. "Oral immunization with recombinant Lactobacillus plantarum expressing Nudix hydrolase and 43 kDa proteins confers protection against Trichinella spiralis in BALB/c mice." Acta Tropica 220 (August 2021): 105947. http://dx.doi.org/10.1016/j.actatropica.2021.105947.

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8

Awile, Omar, Anita Krisko, Ivo F. Sbalzarini, and Bojan Zagrovic. "Intrinsically Disordered Regions May Lower the Hydration Free Energy in Proteins: A Case Study of Nudix Hydrolase in the Bacterium Deinococcus radiodurans." PLoS Computational Biology 6, no. 7 (July 15, 2010): e1000854. http://dx.doi.org/10.1371/journal.pcbi.1000854.

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9

Koebnik, Ralf, Antje Krüger, Frank Thieme, Alexander Urban, and Ulla Bonas. "Specific Binding of the Xanthomonas campestris pv. vesicatoria AraC-Type Transcriptional Activator HrpX to Plant-Inducible Promoter Boxes." Journal of Bacteriology 188, no. 21 (August 25, 2006): 7652–60. http://dx.doi.org/10.1128/jb.00795-06.

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ABSTRACT The pathogenicity of the plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria depends on a type III secretion system which is encoded by the 23-kb hrp (hypersensitive response and pathogenicity) gene cluster. Expression of the hrp operons is strongly induced in planta and in a special minimal medium and depends on two regulatory proteins, HrpG and HrpX. In this study, DNA affinity enrichment was used to demonstrate that the AraC-type transcriptional activator HrpX binds to a conserved cis-regulatory element, the plant-inducible promoter (PIP) box (TTCGC-N15-TTCGC), present in the promoter regions of four hrp operons. No binding of HrpX was observed when DNA fragments lacking a PIP box were used. HrpX also bound to a DNA fragment containing an imperfect PIP box (TTCGC-N8-TTCGT). Dinucleotide replacements in each half-site of the PIP box strongly decreased binding of HrpX, while simultaneous dinucleotide replacements in both half-sites completely abolished binding. Based on the complete genome sequence of Xanthomonas campestris pv. vesicatoria, putative plant-inducible promoters consisting of a PIP box and a −10 promoter motif were identified in the promoter regions of almost all HrpX-activated genes. Bioinformatic analyses and reverse transcription-PCR experiments revealed novel HrpX-dependent genes, among them a NUDIX hydrolase gene and several genes with a predicted role in the degradation of the plant cell wall. We conclude that HrpX is the most downstream component of the hrp regulatory cascade, which is proposed to directly activate most genes of the hrpX regulon via binding to corresponding PIP boxes.
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10

Gunawardana, D., V. A. Likic, and K. R. Gayler. "A Comprehensive Bioinformatics Analysis of the Nudix Superfamily inArabidopsis thaliana." Comparative and Functional Genomics 2009 (2009): 1–13. http://dx.doi.org/10.1155/2009/820381.

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Nudix enzymes are a superfamily with a conserved common reaction mechanism that provides the capacity for the hydrolysis of a broad spectrum of metabolites. We used hidden Markov models based on Nudix sequences from the PFAM and PROSITE databases to identify Nudix hydrolases encoded by theArabidopsisgenome. 25 Nudix hydrolases were identified and classified into 11 individual families by pairwise sequence alignments. Intron phases were strikingly conserved in each family. Phylogenetic analysis showed that all multimember families formed monophyletic clusters. Conserved familial sequence motifs were identified with the MEME motif analysis algorithm. One motif (motif 4) was found in three diverse families. All proteins containing motif 4 demonstrated a degree of preference for substrates containing an ADP moiety. We conclude that HMM model-based genome scanning and MEME motif analysis, respectively, can significantly improve the identification and assignment of function of new members of this mechanistically-diverse protein superfamily.
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