1
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Wang H, Feng Y, Lu H. Low-Level Cefepime Exposure Induces High-Level Resistance in Environmental Bacteria: Molecular Mechanism and Evolutionary Dynamics. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:15074-15083. [PMID: 35608924 DOI: 10.1021/acs.est.2c00793] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Antibiotics exert selective pressures on clinically relevant antibiotic resistance. It is critical to understand how antibiotic resistance evolves in environmental microbes exposed to subinhibitory concentrations of antibiotics and whether evolutionary dynamics and emergence of resistance are predictable. In this study, Comamonas testosteroni isolated from wastewater activated sludge were subcultured in a medium containing 10 ng/mL cefepime for 40 days (∼300 generations). Stepwise mutations were accumulated, leading to an ultimate 200-fold increase in the minimum inhibitory concentration (MIC) of cefepime. Early stage mutation in DNA polymerase-encoding gene dnaE2 played an important role in antibiotic resistance evolution. Diverse resistance mechanisms were employed and validated experimentally, including increased efflux, biofilm formation, reduced antibiotic uptake, and drug inactivation. The cefepime minimal selective concentrations (MSCs) and relative fitness of susceptible, intermediate, and resistant mutants were determined. Agent-based modeling of the modified Moran process enabled simulations of resistance evolution and predictions of the emergence time and frequency of resistant mutants. The unraveled cefepime resistance mechanisms could be employed by broader bacteria, and the newly developed model is applicable to the predictions of general resistance evolution. The improved knowledge facilitates the assessment, prediction, and mitigation of antibiotic resistance progression in antibiotic-polluted environments.
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Affiliation(s)
- Hanqing Wang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Youjun Feng
- Departments of Microbiology & General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Huijie Lu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Academy of Ecological Civilization, Zhejiang University, Hangzhou, Zhejiang 310058, China
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2
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Jia Y, Wang J, Ren C, Nahurira R, Khokhar I, Wang J, Fan S, Yan Y. Identification and characterization of a meta-cleavage product hydrolase involved in biphenyl degradation from Arthrobacter sp. YC-RL1. Appl Microbiol Biotechnol 2019; 103:6825-6836. [PMID: 31240368 DOI: 10.1007/s00253-019-09956-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 05/25/2019] [Accepted: 05/28/2019] [Indexed: 12/27/2022]
Abstract
Polychlorinated biphenyls (PCBs) are a group of persistent organic pollutants (POPs) widely existing in the environment. Arthrobacter sp. YC-RL1 is a biphenyl-degrading bacterium that shows metabolic versatility towards aromatic compounds. A 2-hydroxy-6-oxo-6-phenylhexa-2, 4-dienoate (HOPDA) hydrolase (BphD) gene involved in the biodegradation of biphenyl was cloned from strain YC-RL1 and heterologously expressed in Escherichia coli BL21 (DE3). The recombinant BphDYC-RL1 was purified and characterized. BphDYC-RL1 showed the highest activity at 45 °C and pH 7. It was stable under a wide range of temperature (20-50 °C). The enzyme had a Km value of 0.14 mM, Kcat of 11.61 s-1, and Vmax of 0.027 U/mg. Temperature dependence catalysis exhibited a biphasic Arrhenius Plot with a transition at 20 °C. BphDYC-RL1 was inactivated by SDS, Tween 20, Tween 80, Trition X-100, DTT, CHAPS, NBS, PMSF, and DEPC, but insensitive to EDTA. Site-directed mutagenesis of the active-site residues revealed that the catalytic triad residues (Ser115, His275, and Asp247) of BphDYC-RL1 were necessary for its activity. The investigation of BphDYC-RL1 not only provides new potential enzyme resource for the biodegradation of biphenyl but also helps deepen our understanding on the catalytic process and mechanism.
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Affiliation(s)
- Yang Jia
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Junhuan Wang
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chao Ren
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ruth Nahurira
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ibatsam Khokhar
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiayi Wang
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shuanghu Fan
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yanchun Yan
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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3
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Dimitriou PS, Denesyuk AI, Nakayama T, Johnson MS, Denessiouk K. Distinctive structural motifs co-ordinate the catalytic nucleophile and the residues of the oxyanion hole in the alpha/beta-hydrolase fold enzymes. Protein Sci 2018; 28:344-364. [PMID: 30311984 DOI: 10.1002/pro.3527] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/04/2018] [Accepted: 10/08/2018] [Indexed: 12/17/2022]
Abstract
The alpha/beta-hydrolases (ABH) are among the largest structural families of proteins that are found in nature. Although they vary in their sequence and function, the ABH enzymes use a similar acid-base-nucleophile catalytic mechanism to catalyze reactions on different substrates. Because ABH enzymes are biocatalysts with a wide range of potential applications, protein engineering has taken advantage of their catalytic versatility to develop enzymes with industrial applications. This study is a comprehensive analysis of 40 ABH enzyme families focusing on two identified substructures: the nucleophile zone and the oxyanion zone, which co-ordinate the catalytic nucleophile and the residues of the oxyanion hole, and independently reported as critical for the enzymatic activity. We also frequently observed an aromatic cluster near the nucleophile and oxyanion zones, and opposite the ligand-binding site. The nucleophile zone, the oxyanion zone and the residue cluster enriched in aromatic side chains comprise a three-dimensional structural organization that shapes the active site of ABH enzymes and plays an important role in the enzymatic function by structurally stabilizing the catalytic nucleophile and the residues of the oxyanion hole. The structural data support the notion that the aromatic cluster can participate in co-ordination of the catalytic histidine loop, and properly place the catalytic histidine next to the catalytic nucleophile.
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Affiliation(s)
- Polytimi S Dimitriou
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland
| | - Alexander I Denesyuk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland.,Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Toru Nakayama
- Tohoku University, Biomolecular Engineering, Sendai, Miyagi, 980-8579, Japan
| | - Mark S Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland
| | - Konstantin Denessiouk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland.,Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, Turku, 20520, Finland
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4
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A water-assisted nucleophilic mechanism utilized by BphD, the meta-cleavage product hydrolase in biphenyl degradation. J Mol Graph Model 2017; 76:448-455. [DOI: 10.1016/j.jmgm.2017.07.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 07/14/2017] [Accepted: 07/17/2017] [Indexed: 11/22/2022]
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5
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Rauwerdink A, Kazlauskas RJ. How the Same Core Catalytic Machinery Catalyzes 17 Different Reactions: the Serine-Histidine-Aspartate Catalytic Triad of α/β-Hydrolase Fold Enzymes. ACS Catal 2015; 5:6153-6176. [PMID: 28580193 DOI: 10.1021/acscatal.5b01539] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enzymes within a family often catalyze different reactions. In some cases, this variety stems from different catalytic machinery, but in other cases the machinery is identical; nevertheless, the enzymes catalyze different reactions. In this review, we examine the subset of α/β-hydrolase fold enzymes that contain the serine-histidine-aspartate catalytic triad. In spite of having the same protein fold and the same core catalytic machinery, these enzymes catalyze seventeen different reaction mechanisms. The most common reactions are hydrolysis of C-O, C-N and C-C bonds (Enzyme Classification (EC) group 3), but other enzymes are oxidoreductases (EC group 1), acyl transferases (EC group 2), lyases (EC group 4) or isomerases (EC group 5). Hydrolysis reactions often follow the canonical esterase mechanism, but eight variations occur where either the formation or cleavage of the acyl enzyme intermediate differs. The remaining eight mechanisms are lyase-type elimination reactions, which do not have an acyl enzyme intermediate and, in four cases, do not even require the catalytic serine. This diversity of mechanisms from the same catalytic triad stems from the ability of the enzymes to bind different substrates, from the requirements for different chemical steps imposed by these new substrates and, only in about half of the cases, from additional hydrogen bond partners or additional general acids/bases in the active site. This detailed analysis shows that binding differences and non-catalytic residues create new mechanisms and are essential for understanding and designing efficient enzymes.
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Affiliation(s)
- Alissa Rauwerdink
- Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota 55108, United States
| | - Romas J. Kazlauskas
- Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota 55108, United States
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6
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Li Y, Zhang R, Du L, Zhang Q, Wang W. Insight into the catalytic mechanism of meta-cleavage product hydrolase BphD: a quantum mechanics/molecular mechanics study. RSC Adv 2015. [DOI: 10.1039/c5ra09939k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The catalytic mechanism of BphD (the fourth enzyme of the biphenyl catabolic pathway) toward its natural substrate 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) was investigated in atomistic detail by QM/MM approach.
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Affiliation(s)
- Yanwei Li
- Environment Research Institute
- Shandong University
- Jinan 250100
- P. R. China
| | - Ruiming Zhang
- Environment Research Institute
- Shandong University
- Jinan 250100
- P. R. China
| | - Likai Du
- Key Laboratory of Bio-based Materials
- Qingdao Institute of Bio-energy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- P. R. China
| | - Qingzhu Zhang
- Environment Research Institute
- Shandong University
- Jinan 250100
- P. R. China
| | - Wenxing Wang
- Environment Research Institute
- Shandong University
- Jinan 250100
- P. R. China
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7
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Single residues dictate the co-evolution of dual esterases: MCP hydrolases from the α/β hydrolase family. Biochem J 2013; 454:157-66. [PMID: 23750508 DOI: 10.1042/bj20130552] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Several members of the C-C MCP (meta-cleavage product) hydrolase family demonstrate an unusual ability to hydrolyse esters as well as the MCPs (including those from mono- and bi-cyclic aromatics). Although the molecular mechanisms responsible for such substrate promiscuity are starting to emerge, the full understanding of these complex enzymes is far from complete. In the present paper, we describe six distinct α/β hydrolases identified through genomic approaches, four of which demonstrate the unprecedented characteristic of activity towards a broad spectrum of substrates, including p-nitrophenyl, halogenated, fatty acyl, aryl, glycerol, cinnamoyl and carbohydrate esters, lactones, 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate and 2-hydroxy-6-oxohepta-2,4-dienoate. Using structural analysis and site-directed mutagenesis we have identified the three residues (Ser32, Val130 and Trp144) that determine the unusual substrate specificity of one of these proteins, CCSP0084. The results may open up new research avenues into comparative catalytic models, structural and mechanistic studies, and biotechnological applications of MCP hydrolases.
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8
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Ruzzini AC, Bhowmik S, Yam KC, Ghosh S, Bolin JT, Eltis LD. The lid domain of the MCP hydrolase DxnB2 contributes to the reactivity toward recalcitrant PCB metabolites. Biochemistry 2013; 52:5685-5695. [PMID: 23879719 PMCID: PMC3903462 DOI: 10.1021/bi400774m] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DxnB2 and BphD are meta-cleavage product (MCP) hydrolases that catalyze C-C bond hydrolysis of the biphenyl metabolite 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA). BphD is a bottleneck in the bacterial degradation of polychlorinated biphenyls (PCBs) by the Bph catabolic pathway due in part to inhibition by 3-Cl HOPDAs. By contrast, DxnB2 from Sphingomonas wittichii RW1 catalyzes the hydrolysis of 3-Cl HOPDAs more efficiently. X-ray crystallographic studies of the catalytically inactive S105A variant of DxnB2 complexed with 3-Cl HOPDA revealed a binding mode in which C1 through C6 of the dienoate are coplanar. The chlorine substituent is accommodated by a hydrophobic pocket that is larger than the homologous site in BphDLB400 from Burkholderia xenovorans LB400. The planar binding mode observed in the crystalline complex was consistent with the hyper- and hypsochromically shifted absorption spectra of 3-Cl and 3,9,11-triCl HOPDA, respectively, bound to S105A in solution. Moreover, ES(red), an intermediate possessing a bathochromically shifted spectrum observed in the turnover of HOPDA, was not detected, suggesting that substrate destabilization was rate-limiting in the turnover of these PCB metabolites. Interestingly, electron density for the first α-helix of the lid domain was poorly defined in the dimeric DxnB2 structures, unlike in the tetrameric BphDLB400. Structural comparison of MCP hydrolases identified the NC-loop, connecting the lid to the α/β-hydrolase core domain, as a determinant in the oligomeric state and suggests its involvement in catalysis. Finally, an increased mobility of the DxnB2 lid may contribute to the enzyme's ability to hydrolyze PCB metabolites, highlighting how lid architecture contributes to substrate specificity in α/β-hydrolases.
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Affiliation(s)
- Antonio C. Ruzzini
- Department of Biochemistry and Molecular Biology, University of British Columbia, BC, Canada
| | - Shiva Bhowmik
- Purdue Cancer Research Center and Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Katherine C. Yam
- Department of Biochemistry and Molecular Biology, University of British Columbia, BC, Canada
| | - Subhangi Ghosh
- Purdue Cancer Research Center and Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Jeffrey T. Bolin
- Purdue Cancer Research Center and Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Lindsay D. Eltis
- Department of Biochemistry and Molecular Biology, University of British Columbia, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, BC, Canada
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9
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10
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Zhou H, Qu Y, Kong C, Shen E, Wang J, Zhang X, Ma Q, Zhou J. The key role of a non-active-site residue Met148 on the catalytic efficiency of meta-cleavage product hydrolase BphD. Appl Microbiol Biotechnol 2013; 97:10399-411. [PMID: 23494625 DOI: 10.1007/s00253-013-4814-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 02/21/2013] [Accepted: 02/26/2013] [Indexed: 11/26/2022]
Abstract
meta-Cleavage product (MCP) hydrolases (EC 3.7.1.9) can catalyze a specific C-C bond fission during the microbial aerobic degradation of aromatics. The previous studies on structure-function relationship of MCP hydrolases mainly focus on the active site residues by site-directed mutagenesis. However, the information about the role of the non-active-site residues is still unclear. In this study, a non-active-site residue Met148 of MCP hydrolase BphD was selected as the mutagenesis site according to the sequence alignments, structure superimpose and the tunnel analysis, which underwent the saturation mutagenesis resulting 19 mutants. The catalytic efficiencies of the mutants on 6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) were all decreased compared with the wild-type one except for the M148D mutant. Especially, the M148P mutant exhibited 290-fold lower k cat/K m than that of the wild-type BphD. Transient kinetic analyses of M148P showed the reciprocal relaxation time corresponded to C-C bond cleavage and product release steps (9.6 s(-1)) was 4.08-fold lower than BphD WT (39.2 s(-1)). Tunnel cluster analysis of BphD WT, M148P and M148W demonstrated that only the bulky Trp148 could block tunnel T2 in the BphD WT, but it exhibited slight effects on the catalytic efficiency (0.94-fold of BphD WT). Therefore, product release was not the main reason for the efficiency decrease of M148P. On the other hand, molecular dynamics simulations on the BphD WT and BphD M148P in complex with HOPDA indicated that the dramatic decrease of the catalytic efficiencies of BphD M148P should be due to the unproductive binding of HOPDA. The study demonstrated the catalytic efficiency of MCP hydrolase can be engineered by modification of non-active site residue.
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Affiliation(s)
- Hao Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
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11
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Tuning the substrate selectivity of meta-cleavage product hydrolase by domain swapping. Appl Microbiol Biotechnol 2012; 97:5343-50. [DOI: 10.1007/s00253-012-4405-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 08/29/2012] [Accepted: 09/04/2012] [Indexed: 10/27/2022]
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12
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Ruzzini AC, Horsman GP, Eltis LD. The Catalytic Serine of meta-Cleavage Product Hydrolases Is Activated Differently for C–O Bond Cleavage Than for C–C Bond Cleavage. Biochemistry 2012; 51:5831-40. [DOI: 10.1021/bi300663r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Antonio C. Ruzzini
- Department of Biochemistry
and Molecular Biology and
Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver,
British Columbia V6T 1Z3, Canada
| | - Geoff P. Horsman
- Department of Biochemistry
and Molecular Biology and
Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver,
British Columbia V6T 1Z3, Canada
| | - Lindsay D. Eltis
- Department of Biochemistry
and Molecular Biology and
Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver,
British Columbia V6T 1Z3, Canada
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13
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Knapik AA, Petkowski JJ, Otwinowski Z, Cymborowski MT, Cooper DR, Majorek KA, Chruszcz M, Krajewska WM, Minor W. A multi-faceted analysis of RutD reveals a novel family of α/β hydrolases. Proteins 2012; 80:2359-68. [PMID: 22641504 DOI: 10.1002/prot.24122] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 05/09/2012] [Accepted: 05/14/2012] [Indexed: 11/05/2022]
Abstract
The rut pathway of pyrimidine catabolism is a novel pathway that allows pyrimidine bases to serve as the sole nitrogen source in suboptimal temperatures. The rut operon in E. coli evaded detection until 2006, yet consists of seven proteins named RutA, RutB, etc. through RutG. The operon is comprised of a pyrimidine transporter and six enzymes that cleave and further process the uracil ring. Herein, we report the structure of RutD, a member of the α/β hydrolase superfamily, which is proposed to enhance the rate of hydrolysis of aminoacrylate, a toxic side product of uracil degradation, to malonic semialdehyde. Although this reaction will occur spontaneously in water, the toxicity of aminoacrylate necessitates catalysis by RutD for efficient growth with uracil as a nitrogen source. RutD has a novel and conserved arrangement of residues corresponding to the α/β hydrolase active site, where the nucleophile's spatial position occupied by Ser, Cys, or Asp of the canonical catalytic triad is replaced by histidine. We have used a combination of crystallographic structure determination, modeling and bioinformatics, to propose a novel mechanism for this enzyme. This approach also revealed that RutD represents a previously undescribed family within the α/β hydrolases. We compare and contrast RutD with PcaD, which is the closest structural homolog to RutD. PcaD is a 3-oxoadipate-enol-lactonase with a classic arrangement of residues in the active site. We have modeled a substrate in the PcaD active site and proposed a reaction mechanism.
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Affiliation(s)
- Aleksandra A Knapik
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22903, USA
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14
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Ruzzini AC, Ghosh S, Horsman GP, Foster LJ, Bolin JT, Eltis LD. Identification of an Acyl-Enzyme Intermediate in a meta-Cleavage Product Hydrolase Reveals the Versatility of the Catalytic Triad. J Am Chem Soc 2012; 134:4615-24. [DOI: 10.1021/ja208544g] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Antonio C. Ruzzini
- Department
of Biochemistry and
Molecular Biology, University of British Columbia, Vancouver BC V6T 1Z3, Canada
| | - Subhangi Ghosh
- Purdue Cancer Research Center
and Markey Center for Structural Biology, Department of Biological
Sciences, Purdue University, West Lafayette,
Indiana 47907, United States
| | - Geoff P. Horsman
- Department
of Biochemistry and
Molecular Biology, University of British Columbia, Vancouver BC V6T 1Z3, Canada
| | - Leonard J. Foster
- Department
of Biochemistry and
Molecular Biology, University of British Columbia, Vancouver BC V6T 1Z3, Canada
| | - Jeffrey T. Bolin
- Purdue Cancer Research Center
and Markey Center for Structural Biology, Department of Biological
Sciences, Purdue University, West Lafayette,
Indiana 47907, United States
| | - Lindsay D. Eltis
- Department
of Biochemistry and
Molecular Biology, University of British Columbia, Vancouver BC V6T 1Z3, Canada
- Department of Microbiology and
Immunology, University of British Columbia, Vancouver BC V6T 1Z3, Canada
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15
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McCulloch KM, Mukherjee T, Begley TP, Ealick SE. Structure determination and characterization of the vitamin B6 degradative enzyme (E)-2-(acetamidomethylene)succinate hydrolase. Biochemistry 2010; 49:1226-35. [PMID: 20099871 DOI: 10.1021/bi901812p] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The gene identification and kinetic characterization of (E)-2-(acetamidomethylene)succinate (E-2AMS) hydrolase has recently been described. This enzyme catalyzes the final reaction in the degradation of vitamin B(6) and produces succinic semialdehyde, acetate, ammonia, and carbon dioxide from E-2AMS. The structure of E-2AMS hydrolase was determined to 2.3 A using SAD phasing. E-2AMS hydrolase is a member of the alpha/beta hydrolase superfamily and utilizes a serine/histidine/aspartic acid catalytic triad. Mutation of either the nucleophilic serine or the aspartate resulted in inactive enzyme. Mutation of an additional serine residue in the active site causes the enzyme to be unstable and is likely structurally important. The structure also provides insight into the mechanism of hydrolysis of E-2AMS and identifies several potential catalytically important residues.
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Affiliation(s)
- Kathryn M McCulloch
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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16
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Li A, Qu Y, Zhou J, Ma F, Zhou H, Shi S. Characterization of a novel meta-fission product hydrolase from Dyella ginsengisoli LA-4. Process Biochem 2010. [DOI: 10.1016/j.procbio.2009.08.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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17
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Khajamohiddin S, Repalle ER, Pinjari AB, Merrick M, Siddavattam D. Biodegradation of aromatic compounds: an overview of meta-fission product hydrolases. Crit Rev Microbiol 2008; 34:13-31. [PMID: 18259978 DOI: 10.1080/10408410701683656] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Meta fission product (MFP) hydrolases catalyze hydrolysis of a low reactive carbon-carbon bond found in meta-fission products, generated during biodegradation of various aromatic compounds. These enzymes belong to the alpha/beta hydrolase super family and show structural conservation despite having poor sequence similarity. MFP-hydrolases are substrate specific and studies have indicated that this substrate specificity plays a key role in the determination of the organism's ability to degrade a particular substrate. In this concise review of MFP-hydrolases we discuss their classification, biochemical properties, the molecular basis of their substrate specificity, their catalytic mechanism, and evolutionary significance.
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Affiliation(s)
- Syed Khajamohiddin
- Department of Animal Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
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18
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Li C, Hassler M, Bugg TDH. Catalytic Promiscuity in the α/β-Hydrolase Superfamily: Hydroxamic Acid Formation, CC Bond Formation, Ester and Thioester Hydrolysis in the CC Hydrolase Family. Chembiochem 2008; 9:71-6. [DOI: 10.1002/cbic.200700428] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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19
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Izumi A, Rea D, Adachi T, Unzai S, Park SY, Roper DI, Tame JRH. Structure and Mechanism of HpcG, a Hydratase in the Homoprotocatechuate Degradation Pathway of Escherichia coli. J Mol Biol 2007; 370:899-911. [PMID: 17559873 DOI: 10.1016/j.jmb.2007.05.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2007] [Revised: 05/01/2007] [Accepted: 05/03/2007] [Indexed: 10/23/2022]
Abstract
HpcG catalyses the hydration of a carbon-carbon double bond without the aid of any cofactor other than a simple divalent metal ion such as Mg(2+). Since the substrate has a nearby carbonyl group, it is believed that it first isomerises to form a pair of conjugated double bonds in the enol tautomer before Michael addition of water. Previous chemical studies of the reaction, and that of the related enzyme MhpD, have failed to provide a clear picture of the mechanism. The substrate itself is unstable, preventing co-crystallisation or soaking of crystals, but oxalate is a strong competitive inhibitor. We have solved the crystal structure of the protein in the apo form, and with magnesium and oxalate bound. Modelling substrate into the active site suggests the attacking water molecule is not part of the metal coordination shell, in contrast to a previous proposal. Our model suggests that geometrically strained cis isomer intermediates do not lie on the reaction pathway, and that separate groups are involved in the isomerisation and hydration steps.
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Affiliation(s)
- Atsushi Izumi
- Protein Design Laboratory, Yokohama City University, Suehiro 1-7-29, Tsurumi, Yokohama 230-0045, Japan
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