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Автор: Grafiati

Опубліковано: 8 червня 2024

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1

Nishioka, Tuguhiro, Makoto Iwata, Takuya Imaoka, Maiko Mutoh, Yoshihiro Egashira, Takashi Nishiyama, Takashi Shin, and Takao Fujii. "A Mono-2-Ethylhexyl Phthalate Hydrolase from a Gordonia sp. That Is Able To Dissimilate Di-2-Ethylhexyl Phthalate." Applied and Environmental Microbiology 72, no. 4 (April 2006): 2394–99. http://dx.doi.org/10.1128/aem.72.4.2394-2399.2006.

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ABSTRACT Gordonia sp. strain P8219, a strain able to decompose di-2-ethylhexyl phthalate, was isolated from machine oil-contaminated soil. Mono-2-ethylhexyl phthalate hydrolase was purified from cell extracts of this strain. This enzyme was a 32,164-Da homodimeric protein, and it effectively hydrolyzed monophthalate esters, such as monoethyl, monobutyl, monohexyl, and mono-2-ethylhexyl phthalate. The Km and V max values for mono-2-ethylhexyl phthalate were 26.9 ± 4.3 μM and 18.1 ± 0.9 μmol/min · mg protein, respectively. The deduced amino acid sequence of the enzyme exhibited less than 30% homology with those of meta-cleavage hydrolases which are serine hydrolases but exhibited no significant homology with the sequences of serine esterases. The pentapeptide motif GXSXG, which is conserved in serine hydrolases, was present in the sequence. The enzymatic properties and features of the primary structure suggested that this enzyme is a novel enzyme belonging to an independent group of serine hydrolases.

2

Jeremy Johnson, R., Andrew Bartels, Rachel Erkilla, Nicole Green, Steven Han, Nathaniel Holt, Melissa Jones, et al. "Proteopedia entry: Mammalian serine hydrolases." Biochemistry and Molecular Biology Education 43, no. 1 (November 18, 2014): 60–61. http://dx.doi.org/10.1002/bmb.20840.

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3

Botos, Istvan, and Alexander Wlodawer. "The expanding diversity of serine hydrolases." Current Opinion in Structural Biology 17, no. 6 (December 2007): 683–90. http://dx.doi.org/10.1016/j.sbi.2007.08.003.

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4

Tang, Shan, Adam T. Beattie, Lucie Kafkova, Gianluca Petris, Nicolas Huguenin-Dezot, Marc Fiedler, Matthew Freeman, and Jason W. Chin. "Mechanism-based traps enable protease and hydrolase substrate discovery." Nature 602, no. 7898 (February 16, 2022): 701–7. http://dx.doi.org/10.1038/s41586-022-04414-9.

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AbstractHydrolase enzymes, including proteases, are encoded by 2–3% of the genes in the human genome and 14% of these enzymes are active drug targets1. However, the activities and substrate specificities of many proteases—especially those embedded in membranes—and other hydrolases remain unknown. Here we report a strategy for creating mechanism-based, light-activated protease and hydrolase substrate traps in complex mixtures and live mammalian cells. The traps capture substrates of hydrolases, which normally use a serine or cysteine nucleophile. Replacing the catalytic nucleophile with genetically encoded 2,3-diaminopropionic acid allows the first step reaction to form an acyl-enzyme intermediate in which a substrate fragment is covalently linked to the enzyme through a stable amide bond2; this enables stringent purification and identification of substrates. We identify new substrates for proteases, including an intramembrane mammalian rhomboid protease RHBDL4 (refs. 3,4). We demonstrate that RHBDL4 can shed luminal fragments of endoplasmic reticulum-resident type I transmembrane proteins to the extracellular space, as well as promoting non-canonical secretion of endogenous soluble endoplasmic reticulum-resident chaperones. We also discover that the putative serine hydrolase retinoblastoma binding protein 9 (ref. 5) is an aminopeptidase with a preference for removing aromatic amino acids in human cells. Our results exemplify a powerful paradigm for identifying the substrates and activities of hydrolase enzymes.

5

Liu, Y., M. P. Patricelli, and B. F. Cravatt. "Activity-based protein profiling: The serine hydrolases." Proceedings of the National Academy of Sciences 96, no. 26 (December 21, 1999): 14694–99. http://dx.doi.org/10.1073/pnas.96.26.14694.

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6

Ross, Matthew K., and Ran Wang. "Expanding the Toolkit for the Serine Hydrolases." Chemistry & Biology 22, no. 7 (July 2015): 808–9. http://dx.doi.org/10.1016/j.chembiol.2015.07.002.

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7

Hernáez, M. J., E. Andújar, J. L. Ríos, S. R. Kaschabek, W. Reineke, and E. Santero. "Identification of a Serine Hydrolase Which Cleaves the Alicyclic Ring of Tetralin." Journal of Bacteriology 182, no. 19 (October 1, 2000): 5448–53. http://dx.doi.org/10.1128/jb.182.19.5448-5453.2000.

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ABSTRACT A gene designated thnD, which is required for biodegradation of the organic solvent tetralin by Sphingomonas macrogoltabidus strain TFA, has been identified. Sequence comparison analysis indicated that thnD codes for a carbon-carbon bond serine hydrolase showing highest similarity to hydrolases involved in biodegradation of biphenyl. An insertion mutant defective in ThnD accumulates the ring fission product which results from the extradiol cleavage of the aromatic ring of dihydroxytetralin. The gene product has been purified and characterized. ThnD is an octameric thermostable enzyme with an optimum reaction temperature at 65°C. ThnD efficiently hydrolyzes the ring fission intermediate of the tetralin pathway and also 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid, the ring fission product of the biphenylmeta-cleavage pathway. However, it is not active towards the equivalent intermediates of meta-cleavage pathways of monoaromatic compounds which have small substituents in C-6. When ThnD hydrolyzes the intermediate in the tetralin pathway, it cleaves a C-C bond comprised within the alicyclic ring of tetralin instead of cleaving a linear C-C bond, as all other known hydrolases ofmeta-cleavage pathways do. The significance of this activity of ThnD for the requirement of other activities to mineralize tetralin is discussed.

8

Bernhardt, Peter, Karl Hult, and Romas J. Kazlauskas. "Molecular Basis of Perhydrolase Activity in Serine Hydrolases." Angewandte Chemie International Edition 44, no. 18 (April 29, 2005): 2742–46. http://dx.doi.org/10.1002/anie.200463006.

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9

Bernhardt, Peter, Karl Hult, and Romas J. Kazlauskas. "Molecular Basis of Perhydrolase Activity in Serine Hydrolases." Angewandte Chemie 117, no. 18 (April 29, 2005): 2802–6. http://dx.doi.org/10.1002/ange.200463006.

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10

Patočka, Jiří, Kamil Kuča, and Daniel Jun. "Acetylcholinesterase and Butyrylcholinesterase – Important Enzymes of Human Body." Acta Medica (Hradec Kralove, Czech Republic) 47, no. 4 (2004): 215–28. http://dx.doi.org/10.14712/18059694.2018.95.

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The serine hydrolases and proteases are a ubiquitous group of enzymes that is fundamental to many critical lifefunctions. Human tissues have two distinct cholinesterase activities: acetylcholinesterase and butyrylcholinesterase. Acetylcholinesterase functions in the transmission of nerve impulses, whereas the physiological function of butyrylcholinesterase remains unknown. Acetylcholinesterase is one of the crucial enzymes in the central and peripheral nerve system. Organophosphates and carbamates are potent inhibitors of serine hydrolases and well suited probes for investigating the chemical reaction mechanism of the inhibition. Understanding the enzyme’s chemistry is essential in preventing and/or treating organophosphate and carbamate poisoning as well as designing new medicaments for cholinergic-related diseases like as Alzheimer’s disease.

11

Martínez, Virginia, Fernando de la Peña, Javier García-Hidalgo, Isabel de la Mata, José Luis García, and María Auxiliadora Prieto. "Identification and Biochemical Evidence of a Medium-Chain-Length Polyhydroxyalkanoate Depolymerase in the Bdellovibrio bacteriovorus Predatory Hydrolytic Arsenal." Applied and Environmental Microbiology 78, no. 17 (June 15, 2012): 6017–26. http://dx.doi.org/10.1128/aem.01099-12.

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ABSTRACTThe obligate predatorBdellovibrio bacteriovorusHD100 shows a large set of proteases and other hydrolases as part of its hydrolytic arsenal needed for its predatory life cycle. We present genetic and biochemical evidence that open reading frame (ORF) Bd3709 ofB. bacteriovorusHD100 encodes a novel medium-chain-length polyhydroxyalkanoate (mcl-PHA) depolymerase (PhaZBd). The primary structure of PhaZBdsuggests that this enzyme belongs to the α/β-hydrolase fold family and has a typical serine hydrolase catalytic triad (serine-histidine-aspartic acid) in agreement with other PHA depolymerases and lipases. PhaZBdhas been extracellularly produced using different hypersecretor Tol-pal mutants ofEscherichia coliandPseudomonas putidaas recombinant hosts. The recombinant PhaZBdhas been characterized, and its biochemical properties have been compared to those of other PHA depolymerases. The enzyme behaves as a serine hydrolase that is inhibited by phenylmethylsulfonyl fluoride. It is also affected by the reducing agent dithiothreitol and nonionic detergents like Tween 80. PhaZBdis an endoexohydrolase that cleaves both large and small PHA molecules, producing mainly dimers but also monomers and trimers. The enzyme specifically degrades mcl-PHA and is inactive toward short-chain-length polyhydroxyalkanoates (scl-PHA) like polyhydroxybutyrate (PHB). These studies shed light on the potentiality of these predators as sources of new biocatalysts, such as an mcl-PHA depolymerase, for the production of enantiopure hydroxyalkanoic acids and oligomers as building blocks for the synthesis of biobased polymers.

12

Chen, Biao, Sha-Sha Ge, Yuan-Chao Zhao, Chong Chen, and Song Yang. "Activity-based protein profiling: an efficient approach to study serine hydrolases and their inhibitors in mammals and microbes." RSC Advances 6, no. 114 (2016): 113327–43. http://dx.doi.org/10.1039/c6ra20006k.

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13

Berger, Natascha, Hanna Allerkamp, and Christian Wadsack. "Serine Hydrolases in Lipid Homeostasis of the Placenta-Targets for Placental Function?" International Journal of Molecular Sciences 23, no. 12 (June 20, 2022): 6851. http://dx.doi.org/10.3390/ijms23126851.

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The metabolic state of pregnant women and their unborn children changes throughout pregnancy and adapts to the specific needs of each gestational week. These adaptions are accomplished by the actions of enzymes, which regulate the occurrence of their endogenous substrates and products in all three compartments: mother, placenta and the unborn. These enzymes determine bioactive lipid signaling, supply, and storage through the generation or degradation of lipids and fatty acids, respectively. This review focuses on the role of lipid-metabolizing serine hydrolases during normal pregnancy and in pregnancy-associated pathologies, such as preeclampsia, gestational diabetes mellitus, or preterm birth. The biochemical properties of each class of lipid hydrolases are presented, with special emphasis on their role in placental function or dysfunction. While, during a normal pregnancy, an appropriate tonus of bioactive lipids prevails, dysregulation and aberrant signaling occur in diseased states. A better understanding of the dynamics of serine hydrolases across gestation and their involvement in placental lipid homeostasis under physiological and pathophysiological conditions will help to identify new targets for placental function in the future.

14

Schirmer, Andreas, Claudia Matz, and Dieter Jendrossek. "Substrate specificities of poly(hydroxyalkanoate)-degrading bacteria and active site studies on the extracellular poly(3-hydroxyoctanoic acid) depolymerase of Pseudomonas fluorescens GK13." Canadian Journal of Microbiology 41, no. 13 (December 15, 1995): 170–79. http://dx.doi.org/10.1139/m95-184.

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The isolation of poly(3-hydroxyoctanoic acid)- and poly(6-hydroxyhexanoic acid)-degrading bacteria yielded 28 strains with abilities to degrade various polymers. The most versatile strains hydrolyzed five different polyesters comprising short chain length and medium chain length poly(hydroxyalkanoates). The new isolates together with previously isolated poly(hydroxyalkanoate)-degrading bacteria were classified into 11 groups with respect to their polymer-degrading specificities. All PHA depolymerases studied so far have been characterized by the lipase consensus sequence Gly-X-Ser-X-Gly in their amino acid sequence, which is a known sequence for serine hydrolases. When we replaced the central residue, Ser-172, in the corresponding sequence Gly-Ile-Ser-Ser-Gly of the extracellular poly(3-hydroxyoctanoic acid) depolymerase of Pseudomonas fluorescens GK13, with alanine the enzyme lost its activity completely. This result of the mutational experiment indicates that the poly(3-hydroxyoctanoic acid) depolymerase belongs to the family of serine hydrolases.Key words: poly(hydroxyalkanoates), PHA depolymerases, serine hydrolases, substrate specificity, Pseudomonas fluorescens.

15

Bachovchin, Daniel A., and Benjamin F. Cravatt. "The pharmacological landscape and therapeutic potential of serine hydrolases." Nature Reviews Drug Discovery 11, no. 1 (January 2012): 52–68. http://dx.doi.org/10.1038/nrd3620.

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16

van Rantwijk, Fred, and Roger A. Sheldon. "Enantioselective acylation of chiral amines catalysed by serine hydrolases." Tetrahedron 60, no. 3 (January 2004): 501–19. http://dx.doi.org/10.1016/j.tet.2003.10.018.

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17

Cognetta, Armand B., Micah J. Niphakis, Hyeon-Cheol Lee, Michael L. Martini, Jonathan J. Hulce, and Benjamin F. Cravatt. "Selective N-Hydroxyhydantoin Carbamate Inhibitors of Mammalian Serine Hydrolases." Chemistry & Biology 22, no. 7 (July 2015): 928–37. http://dx.doi.org/10.1016/j.chembiol.2015.05.018.

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18

Fischer, Frank, Stefan Künne та Susanne Fetzner. "Bacterial 2,4-Dioxygenases: New Members of the α/β Hydrolase-Fold Superfamily of Enzymes Functionally Related to Serine Hydrolases". Journal of Bacteriology 181, № 18 (15 вересня 1999): 5725–33. http://dx.doi.org/10.1128/jb.181.18.5725-5733.1999.

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ABSTRACT 1H-3-hydroxy-4-oxoquinoline 2,4-dioxygenase (Qdo) fromPseudomonas putida 33/1 and 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase (Hod) fromArthrobacter ilicis Rü61a catalyze an N-heterocyclic-ring cleavage reaction, generatingN-formylanthranilate and N-acetylanthranilate, respectively, and carbon monoxide. Amino acid sequence comparisons between Qdo, Hod, and a number of proteins belonging to the α/β hydrolase-fold superfamily of enzymes and analysis of the similarity between the predicted secondary structures of the 2,4-dioxygenases and the known secondary structure of haloalkane dehalogenase fromXanthobacter autotrophicus GJ10 strongly suggested that Qdo and Hod are structurally related to the α/β hydrolase-fold enzymes. The residues S95 and H244 of Qdo were found to be arranged like the catalytic nucleophilic residue and the catalytic histidine, respectively, of the α/β hydrolase-fold enzymes. Investigation of the potential functional significance of these and other residues of Qdo through site-directed mutagenesis supported the hypothesis that Qdo is structurally as well as functionally related to serine hydrolases, with S95 being a possible catalytic nucleophile and H244 being a possible catalytic base. A hypothetical reaction mechanism for Qdo-catalyzed 2,4-dioxygenolysis, involving formation of an ester bond between the catalytic serine residue and the carbonyl carbon of the substrate and subsequent dioxygenolysis of the covalently bound anionic intermediate, is discussed.

19

GLYNN, Paul. "Neuropathy target esterase." Biochemical Journal 344, no. 3 (December 8, 1999): 625–31. http://dx.doi.org/10.1042/bj3440625.

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Neuropathy target esterase (NTE) is an integral membrane protein present in all neurons and in some non-neural-cell types of vertebrates. Recent data indicate that NTE is involved in a cell-signalling pathway controlling interactions between neurons and accessory glial cells in the developing nervous system. NTE has serine esterase activity and efficiently catalyses the hydrolysis of phenyl valerate (PV) in vitro, but its physiological substrate is unknown. By sequence analysis NTE has been found to be related neither to the major serine esterase family, which includes acetylcholinesterase, nor to any other known serine hydrolases. NTE comprises at least two functional domains: an N-terminal putative regulatory domain and a C-terminal effector domain which contains the esterase activity and is, in part, conserved in proteins found in bacteria, yeast, nematodes and insects. NTE's effector domain contains three predicted transmembrane segments, and the active-site serine residue lies at the centre of one of these segments. The isolated recombinant domain shows PV hydrolase activity only when incorporated into phospholipid liposomes. NTE's esterase activity appears to be largely redundant in adult vertebrates, but organophosphates which react with NTE in vivo initiate unknown events which lead, after a delay of 1-3 weeks, to a neuropathy with degeneration of long axons. These neuropathic organophosphates leave a negatively charged group covalently attached to the active-site serine residue, and it is suggested that this may cause a toxic gain of function in NTE.

20

Otrubova, Katerina, Venkat Srinivasan, and Dale L. Boger. "Discovery libraries targeting the major enzyme classes: The serine hydrolases." Bioorganic & Medicinal Chemistry Letters 24, no. 16 (August 2014): 3807–13. http://dx.doi.org/10.1016/j.bmcl.2014.06.063.

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21

Cai, Yu-dong, Guo-Ping Zhou, Chin-Hung Jen, Shuo-Liang Lin, and Kuo-Chen Chou. "Identify catalytic triads of serine hydrolases by support vector machines." Journal of Theoretical Biology 228, no. 4 (June 2004): 551–57. http://dx.doi.org/10.1016/j.jtbi.2004.02.019.

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22

Otrubova, Katerina, Shreyosree Chatterjee, Srijana Ghimire, Benjamin F. Cravatt, and Dale L. Boger. "N-Acyl pyrazoles: Effective and tunable inhibitors of serine hydrolases." Bioorganic & Medicinal Chemistry 27, no. 8 (April 2019): 1693–703. http://dx.doi.org/10.1016/j.bmc.2019.03.020.

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23

Field, S. Denise, Wankyu Lee, Jason K. Dutra, Finley Scott F. Serneo, Jon Oyer, Hua Xu, Douglas S. Johnson, Christopher W. am Ende, and Uthpala Seneviratne. "Fluorophosphonate‐Based Degrader Identifies Degradable Serine Hydrolases by Quantitative Proteomics." ChemBioChem 21, no. 20 (July 23, 2020): 2916–20. http://dx.doi.org/10.1002/cbic.202000253.

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24

Jiang, Yun, Krista L. Morley, Joseph D. Schrag, and Romas J. Kazlauskas. "Different Active-Site Loop Orientation in Serine Hydrolases versus Acyltransferases." ChemBioChem 12, no. 5 (February 23, 2011): 768–76. http://dx.doi.org/10.1002/cbic.201000693.

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25

Xu, Hao, Hairat Sabit, Gordon L. Amidon, and H. D. Hollis Showalter. "An improved synthesis of a fluorophosphonate–polyethylene glycol–biotin probe and its use against competitive substrates." Beilstein Journal of Organic Chemistry 9 (January 15, 2013): 89–96. http://dx.doi.org/10.3762/bjoc.9.12.

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The fluorophosphonate (FP) moiety attached to a biotin tag is a prototype chemical probe used to quantitatively analyze and enrich active serine hydrolases in complex proteomes in an approach called activity-based protein profiling (ABPP). In this study we have designed a novel synthetic route to a known FP probe linked by polyethylene glycol to a biotin tag (FP–PEG–biotin). Our route markedly increases the efficiency of the probe synthesis and overcomes several problems of a prior synthesis. As a proof of principle, FP–PEG–biotin was evaluated against isolated protein mixtures and different rat-tissue homogenates, showing its ability to specifically target serine hydrolases. We also assessed the ability of FP–PEG–biotin to compete with substrates that have high enzyme turnover rates. The reduced protein-band intensities resulting in these competition studies demonstrate a new application of FP-based probes seldom explored before.

26

Arastu-Kapur, Shirin, Kevin Shenk, Francesco Parlati, and Mark K. Bennett. "Non-Proteasomal Targets of Proteasome Inhibitors Bortezomib and Carfilzomib." Blood 112, no. 11 (November 16, 2008): 2657. http://dx.doi.org/10.1182/blood.v112.11.2657.2657.

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Abstract The proteasome is a multicatalytic protease complex that has been validated as a therapeutic target in oncology with the approval of bortezomib for the treatment of multiple myeloma and mantle cell lymphoma. Carfilzomib is a next generation proteasome inhibitor that is structurally and mechanistically distinct from bortezomib and has entered clinical development in oncology. Both inhibitors target the chymotrypsin-like activity of the proteasome, but their mechanism of action differs due to their unique chemical pharmacores (or “warheads”): bortezomib is a boronate while carfilzomib is an epoxyketone. Phase 1 studies with carfilzomib suggest a clinical safety profile that has both commonalities and distinctions from bortezomib. Transient thrombocytopenia is observed with both molecules suggesting that this event is a proteasome inhibitor class effect. In contrast, the painful peripheral neuropathy that is commonly observed with bortezomib appears to be less severe and possibly less frequent with carfilzomib, raising the possibility that non-proteasome mechanisms may underlie this toxicity. To gain potential insight into the common and unique clinical toxicities of bortezomib and carfilzomib, we evaluated their propensity to act as inhibitors of non-proteasomal enzymes. Bortezomib and carfilzomib were initially screened in a panel of candidate cysteine, aspartyl, metallo-, and serine proteases. Bortezomib significantly inhibited the serine proteases cathepsin G (IC50= 0.3μM) and chymase (IC50= 1.1μM), while carfilzomib did not inhibit these enzymes (IC50>10μM). These effects were further validated in cell extracts prepared from the Thp1 monocyte cell line and peripheral blood mononuclear cells (PBMC), where the inhibition of cathepsin G and chymase by bortezomib was detected using FP-biotin, a serine hydrolase-specific fluorophosphonate activity-based probe. These results suggest that the boronic acid warhead of bortezomib has greater off-target activity than the epoxyketone warhead of carfilzomib. To further investigate this hypothesis, off-target binding of proteasome inhibitors with either the boronate (Cbz-LLL-boronate) or epoxyketone (Cbz-LLL-epoxyketone) warheads were tested in cell extracts and intact cells using FP-biotin detection. Several serine hydrolases in liver (HepG2), lung (A549), kidney (786-O), and leukemia (Thp1) tumor cell lines were found to bind the boronate inhibitor but not the epoxyketone inhibitor. This result suggests that the boronate warhead is more “promiscuous” than the expoxyketone warhead. To obtain a global inhibition profile of the serine hydrolases that are targeted by bortezomib, multidimensional protein identification technology (MudPIT) analysis was performed on FP-biotin-reactive proteins from HepG2 cell extracts. Bortezomib was found to bind several serine hydrolases, including cathepsin A and dipeptidyl peptidase IV (DPP IV) and we have further validated these targets using specific antibodies. Taken together, these data demonstrate that non-proteasomal enzymes can be targeted by bortezomib (cathepsin G, cathepsin A, DPP IV and chymase), whereas carfilzomib does not appear to inhibit non-proteasomal targets in our assays. Work in progress includes biochemical and cell-based characterization for non-proteasomal targets, further global proteomic inhibition profiling using MudPIT analyses, and assessing the potential contribution of non-proteasomal targets to the differential toxicity profiles of the two proteasome inhibitor classes.

27

Willing, Stephanie, Emma Dyer, Olaf Schneewind, and Dominique Missiakas. "FmhA and FmhC of Staphylococcus aureus incorporate serine residues into peptidoglycan cross-bridges." Journal of Biological Chemistry 295, no. 39 (August 5, 2020): 13664–76. http://dx.doi.org/10.1074/jbc.ra120.014371.

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Staphylococcal peptidoglycan is characterized by pentaglycine cross-bridges that are cross-linked between adjacent wall peptides by penicillin-binding proteins to confer robustness and flexibility. In Staphylococcus aureus, pentaglycine cross-bridges are synthesized by three proteins: FemX adds the first glycine, and the homodimers FemA and FemB sequentially add two Gly-Gly dipeptides. Occasionally, serine residues are also incorporated into the cross-bridges by enzymes that have heretofore not been identified. Here, we show that the FemA/FemB homologues FmhA and FmhC pair with FemA and FemB to incorporate Gly-Ser dipeptides into cross-bridges and to confer resistance to lysostaphin, a secreted bacteriocin that cleaves the pentaglycine cross-bridge. FmhA incorporates serine residues at positions 3 and 5 of the cross-bridge. In contrast, FmhC incorporates a single serine at position 5. Serine incorporation also lowers resistance toward oxacillin, an antibiotic that targets penicillin-binding proteins, in both methicillin-sensitive and methicillin-resistant strains of S. aureus. FmhC is encoded by a gene immediately adjacent to lytN, which specifies a hydrolase that cleaves the bond between the fifth glycine of cross-bridges and the alanine of the adjacent stem peptide. In this manner, LytN facilitates the separation of daughter cells. Cell wall damage induced upon lytN overexpression can be alleviated by overexpression of fmhC. Together, these observations suggest that FmhA and FmhC generate peptidoglycan cross-bridges with unique serine patterns that provide protection from endogenous murein hydrolases governing cell division and from bacteriocins produced by microbial competitors.

28

RIDDER, Ivo S., and Bauke W. DIJKSTRA. "Identification of the Mg2+-binding site in the P-type ATPase and phosphatase members of the HAD (haloacid dehalogenase) superfamily by structural similarity to the response regulator protein CheY." Biochemical Journal 339, no. 2 (April 8, 1999): 223–26. http://dx.doi.org/10.1042/bj3390223.

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The large HAD (haloacid dehalogenase) superfamily of hydrolases comprises P-type ATPases, phosphatases, epoxide hydrolases and l-2-haloacid dehalogenases. A comparison of the three-dimensional structure of l-2-haloacid dehalogenase with that of the response regulator protein CheY allowed the assignment of a conserved pair of aspartate residues as the Mg2+-binding site in the P-type ATPase and phosphatase members of the superfamily. From the resulting model of the active site, a conserved serine/threonine residue is suggested to be involved in phosphate binding, and a mechanism comprising a phosphoaspartate intermediate is postulated.

29

Derewenda, Zygmunt S., and Urszula Derewenda. "Relationships among serine hydrolases: evidence for a common structural motif in triacylglyceride lipases and esterases." Biochemistry and Cell Biology 69, no. 12 (December 1, 1991): 842–51. http://dx.doi.org/10.1139/o91-125.

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A detailed analysis of the highly refined (1.9 Å resolution) molecular model of the fungal (Rhizomucor miehei) triglyceride lipase reveals a unique conformation of the oligopeptide containing the active serine (Ser 144) residue. It consists of a six-residue β-strand (strand 4 of the central sheet), a four-residue turn of type II′ with serine in the ε conformation, and a buried α-helix packed in a parallel way against strands 4 and 5 of the central β-pleated sheet. It is shown that the invariant glycines in positions (1) and (5) of the so-called lipase consensus sequence (G-X-S-X-G) are in extended and helical conformations, respectively, and that they are conserved owing to the steric restrictions imposed on these residues by the packing stereochemistry of this β-εSer-α motif, and not by secondary structure requirements, as is the case in serine proteinases. Sequence homologies indicate that this unique motif is likely to be found in serine esterases and other lipases, indicating a possible evolutionary link of these families of hydrolytic enzymes.Key words: serine proteinases, lipases, esterases, protein crystallography, protein structure.

30

Kumar, Kundan, Amol Mhetre, Girish S. Ratnaparkhi, and Siddhesh S. Kamat. "A Superfamily-wide Activity Atlas of Serine Hydrolases in Drosophila melanogaster." Biochemistry 60, no. 16 (April 7, 2021): 1312–24. http://dx.doi.org/10.1021/acs.biochem.1c00171.

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31

Roda, Sergi, Laura Fernandez-Lopez, Rubén Cañadas, Gerard Santiago, Manuel Ferrer, and Victor Guallar. "Computationally Driven Rational Design of Substrate Promiscuity on Serine Ester Hydrolases." ACS Catalysis 11, no. 6 (March 5, 2021): 3590–601. http://dx.doi.org/10.1021/acscatal.0c05015.

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32

Yin, Hequn, Jeffrey P. Jones, and M. W. Anders. "Slow-binding inhibition of carboxylesterase and other serine hydrolases by chlorodifluoroacetaldehyde." Chemical Research in Toxicology 6, no. 5 (September 1993): 630–34. http://dx.doi.org/10.1021/tx00035a007.

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33

Barton, Jennifer Marie, and R. Jeremy Johnson. "Role of conserved serine hydrolases in controlling acetaldehyde toxicity in yeast." FASEB Journal 34, S1 (April 2020): 1. http://dx.doi.org/10.1096/fasebj.2020.34.s1.04367.

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34

Gonzales, C. R., Sahai Srivastava, and J. E. Fitzpatrick. "Diisopropylfluorophosphate Binding Proteins (Serine Hydrolases) from Normal and Leukemic Hematopoietic Cells." Acta Haematologica 84, no. 1 (1990): 5–13. http://dx.doi.org/10.1159/000205019.

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35

Nickel, Sabrina, Farnusch Kaschani, Tom Colby, Renier A. L. van der Hoorn, and Markus Kaiser. "A para-nitrophenol phosphonate probe labels distinct serine hydrolases of Arabidopsis." Bioorganic & Medicinal Chemistry 20, no. 2 (January 2012): 601–6. http://dx.doi.org/10.1016/j.bmc.2011.06.041.

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36

Dijkstra, Harmen P., Hein Sprong, Bas N. H. Aerts, Cornelis A. Kruithof, Maarten R. Egmond, and Robertus J. M. Klein Gebbink. "Selective and diagnostic labelling of serine hydrolases with reactive phosphonate inhibitors." Org. Biomol. Chem. 6, no. 3 (2008): 523–31. http://dx.doi.org/10.1039/b717345h.

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37

Wang, Chao, Daniel Abegg, Brendan G. Dwyer, and Alexander Adibekian. "Discovery and Evaluation of New Activity‐Based Probes for Serine Hydrolases." ChemBioChem 20, no. 17 (July 29, 2019): 2212–16. http://dx.doi.org/10.1002/cbic.201900126.

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38

Rudolf, Bogna, Michèle Salmain, Pierre Haquette, Marcin Stachowicz, and Krzysztof Woźniak. "Novel ferrocenyl phosphonate derivatives. Inhibition of serine hydrolases by ferrocene azaphosphonates." Applied Organometallic Chemistry 24, no. 10 (September 16, 2010): 721–26. http://dx.doi.org/10.1002/aoc.1673.

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39

LUSH, Michael J., Yong LI, David J. READ, Anthony C. WILLIS, and Paul GLYNN. "Neuropathy target esterase and a homologous Drosophila neurodegeneration-associated mutant protein contain a novel domain conserved from bacteria to man." Biochemical Journal 332, no. 1 (May 15, 1998): 1–4. http://dx.doi.org/10.1042/bj3320001.

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The N-terminal amino acid sequences of proteolytic fragments of neuropathy target esterase (NTE), covalently labelled on its active-site serine by a biotinylated organophosphorus ester, were determined and used to deduce the location of this serine residue and to initiate cloning of its cDNA. A putative NTE clone, isolated from a human foetal brain cDNA library, encoded a 1327 residue polypeptide with no homology to any known serine esterases or proteases. The active-site serine of NTE (Ser-966) lay in the centre of a predicted hydrophobic helix within a 200-amino-acid C-terminal domain with marked similarity to conceptual proteins in bacteria, yeast and nematodes; these proteins may comprise a novel family of potential serine hydrolases. The Swiss Cheese protein which, when mutated, leads to widespread cell death in Drosophilabrain [Kretzschmar, Hasan, Sharma, Heisenberg and Benzer (1997) J. Neurosci. 17, 7425–7432], was strikingly homologous to NTE, suggesting that genetically altered NTE may be involved in human neurodegenerative disease.

40

Long, Jonathan Z., and Benjamin F. Cravatt. "The Metabolic Serine Hydrolases and Their Functions in Mammalian Physiology and Disease." Chemical Reviews 111, no. 10 (October 12, 2011): 6022–63. http://dx.doi.org/10.1021/cr200075y.

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41

Shamshurin, Dmitry, Oleg V. Krokhin, David Levin, Richard Sparling, and John A. Wilkins. "In situ activity-based protein profiling of serine hydrolases in E. coli." EuPA Open Proteomics 4 (September 2014): 18–24. http://dx.doi.org/10.1016/j.euprot.2014.04.007.

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42

Kaschani, Farnusch, Sabrina Nickel, Bikram Pandey, Benjamin F. Cravatt, Markus Kaiser, and Renier A. L. van der Hoorn. "Selective inhibition of plant serine hydrolases by agrochemicals revealed by competitive ABPP." Bioorganic & Medicinal Chemistry 20, no. 2 (January 2012): 597–600. http://dx.doi.org/10.1016/j.bmc.2011.06.040.

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43

Makhaeva, G. F., V. V. Malygin, A. Yu Aksinenko, V. B. Sokolov, N. N. Strakhova, A. N. Rasdolsky, R. J. Richardson та I. V. Martynov. "Fluorinated α-aminophosphonates—a new type of irreversible inhibitors of serine hydrolases". Doklady Biochemistry and Biophysics 400, № 1-6 (січень 2005): 92–95. http://dx.doi.org/10.1007/s10628-005-0041-7.

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44

Simon, Gabriel M., and Benjamin F. Cravatt. "Activity-based Proteomics of Enzyme Superfamilies: Serine Hydrolases as a Case Study." Journal of Biological Chemistry 285, no. 15 (February 10, 2010): 11051–55. http://dx.doi.org/10.1074/jbc.r109.097600.

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45

Faucher, Franco, John M. Bennett, Matthew Bogyo, and Scott Lovell. "Strategies for Tuning the Selectivity of Chemical Probes that Target Serine Hydrolases." Cell Chemical Biology 27, no. 8 (August 2020): 937–52. http://dx.doi.org/10.1016/j.chembiol.2020.07.008.

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46

Otte, Nikolaj, Marco Bocola, and Walter Thiel. "Force-field parameters for the simulation of tetrahedral intermediates of serine hydrolases." Journal of Computational Chemistry 30, no. 1 (January 15, 2009): 154–62. http://dx.doi.org/10.1002/jcc.21037.

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47

Ganci, W., U. Ringeisen, and P. Ruedi. "ChemInform Abstract: Synthesis of Rigid Acetylcholine Mimics as Inhibitors of Serine Hydrolases." ChemInform 32, no. 23 (May 26, 2010): no. http://dx.doi.org/10.1002/chin.200123272.

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48

Liu, Hui, Huimin Zhou, Huaqiao Du, Qiaoling Xiao, and Marco Pistolozzi. "Kinetically-controlled mechanism-based isolation of metabolic serine hydrolases in active form from complex proteomes: butyrylcholinesterase as a case study." RSC Advances 9, no. 66 (2019): 38505–19. http://dx.doi.org/10.1039/c9ra07583f.

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49

Hwang, Jisub, Hackwon Do, Youn-Soo Shim, and Jun Hyuck Lee. "Crystal Structure and Functional Characterization of an S-Formylglutathione Hydrolase (BuSFGH) from Burkholderiaceae sp." Crystals 13, no. 4 (April 4, 2023): 621. http://dx.doi.org/10.3390/cryst13040621.

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S-formylglutathione hydrolases (SFGHs) catalyze the hydrolysis of S-formylglutathione to formate and glutathione using the conserved serine hydrolase catalytic triad residues (Ser-His-Asp). SFGHs have broad substrate specificity, including, for example, ester bond-containing substrates. Here, we report the crystal structure of Burkholderiaceae sp. SFGH (BuSFGH) at 1.73 Å resolution. Structural analysis showed that the overall structure of BuSFGH has a typical α/β hydrolase fold, with a central β-sheet surrounded by α-helices. Analytical ultracentrifugation analysis showed that BuSFGH formed a stable dimer in solution. The enzyme activity assay indicated that BuSFGH has a high preference for short-chain p-nitrophenyl esters, such as p-nitrophenyl acetate. The activity of BuSFGH toward p-nitrophenyl acetate was five times higher than that of p-nitrophenyl butylate. Molecular modeling studies on the p-nitrophenyl acetate-bound BuSFGH structure indicate that Gly52, Leu53, Trp96, His147, Ser148, Trp182, Phe228, and His259 residues may be crucial for substrate binding. Collectively, these results are useful for understanding the substrate-binding mechanism and substrate specificity of BuSFGH. They can also provide useful insights for designing modified BuSFGHs with different substrate specificities.

50

Polderman-Tijmes, Jolanda J., Peter A. Jekel, Erik J. de Vries, Annet E. J. van Merode, René Floris, Jan-Metske van der Laan, Theo Sonke та Dick B. Janssen. "Cloning, Sequence Analysis, and Expression in Escherichia coli of the Gene Encoding an α-Amino Acid Ester Hydrolase from Acetobacter turbidans". Applied and Environmental Microbiology 68, № 1 (січень 2002): 211–18. http://dx.doi.org/10.1128/aem.68.1.211-218.2002.

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ABSTRACT The α-amino acid ester hydrolase from Acetobacter turbidans ATCC 9325 is capable of hydrolyzing and synthesizing β-lactam antibiotics, such as cephalexin and ampicillin. N-terminal amino acid sequencing of the purified α-amino acid ester hydrolase allowed cloning and genetic characterization of the corresponding gene from an A. turbidans genomic library. The gene, designated aehA, encodes a polypeptide with a molecular weight of 72,000. Comparison of the determined N-terminal sequence and the deduced amino acid sequence indicated the presence of an N-terminal leader sequence of 40 amino acids. The aehA gene was subcloned in the pET9 expression plasmid and expressed in Escherichia coli. The recombinant protein was purified and found to be dimeric with subunits of 70 kDa. A sequence similarity search revealed 26% identity with a glutaryl 7-ACA acylase precursor from Bacillus laterosporus, but no homology was found with other known penicillin or cephalosporin acylases. There was some similarity to serine proteases, including the conservation of the active site motif, GXSYXG. Together with database searches, this suggested that the α-amino acid ester hydrolase is a β-lactam antibiotic acylase that belongs to a class of hydrolases that is different from the Ntn hydrolase superfamily to which the well-characterized penicillin acylase from E. coli belongs. The α-amino acid ester hydrolase of A. turbidans represents a subclass of this new class of β-lactam antibiotic acylases.