1
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Naz S, Liu P, Farooq U, Ma H. Insight into de-regulation of amino acid feedback inhibition: a focus on structure analysis method. Microb Cell Fact 2023; 22:161. [PMID: 37612753 PMCID: PMC10464499 DOI: 10.1186/s12934-023-02178-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/13/2023] [Indexed: 08/25/2023] Open
Abstract
Regulation of amino acid's biosynthetic pathway is of significant importance to maintain homeostasis and cell functions. Amino acids regulate their biosynthetic pathway by end-product feedback inhibition of enzymes catalyzing committed steps of a pathway. Discovery of new feedback resistant enzyme variants to enhance industrial production of amino acids is a key objective in industrial biotechnology. Deregulation of feedback inhibition has been achieved for various enzymes using in vitro and in silico mutagenesis techniques. As enzyme's function, its substrate binding capacity, catalysis activity, regulation and stability are dependent on its structural characteristics, here, we provide detailed structural analysis of all feedback sensitive enzyme targets in amino acid biosynthetic pathways. Current review summarizes information regarding structural characteristics of various enzyme targets and effect of mutations on their structures and functions especially in terms of deregulation of feedback inhibition. Furthermore, applicability of various experimental as well as computational mutagenesis techniques to accomplish feedback resistance has also been discussed in detail to have an insight into various aspects of research work reported in this particular field of study.
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Affiliation(s)
- Sadia Naz
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Pi Liu
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Umar Farooq
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Islamabad, 22060, Pakistan
| | - Hongwu Ma
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
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2
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Chaudhary D, Singh A, Marzuki M, Ghosh A, Kidwai S, Gosain TP, Chawla K, Gupta SK, Agarwal N, Saha S, Kumar Y, Thakur KG, Singhal A, Singh R. Identification of small molecules targeting homoserine acetyl transferase from Mycobacterium tuberculosis and Staphylococcus aureus. Sci Rep 2022; 12:13801. [PMID: 35963878 PMCID: PMC9376091 DOI: 10.1038/s41598-022-16468-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 07/11/2022] [Indexed: 11/09/2022] Open
Abstract
There is an urgent need to validate new drug targets and identify small molecules that possess activity against both drug-resistant and drug-sensitive bacteria. The enzymes belonging to amino acid biosynthesis have been shown to be essential for growth in vitro, in vivo and have not been exploited much for the development of anti-tubercular agents. Here, we have identified small molecule inhibitors targeting homoserine acetyl transferase (HSAT, MetX, Rv3341) from M. tuberculosis. MetX catalyses the first committed step in L-methionine and S-adenosyl methionine biosynthesis resulting in the formation of O-acetyl-homoserine. Using CRISPRi approach, we demonstrate that conditional repression of metX resulted in inhibition of M. tuberculosis growth in vitro. We have determined steady state kinetic parameters for the acetylation of L-homoserine by Rv3341. We show that the recombinant enzyme followed Michaelis-Menten kinetics and utilizes both acetyl-CoA and propionyl-CoA as acyl-donors. High-throughput screening of a 2443 compound library resulted in identification of small molecule inhibitors against MetX enzyme from M. tuberculosis. The identified lead compounds inhibited Rv3341 enzymatic activity in a dose dependent manner and were also active against HSAT homolog from S. aureus. Molecular docking of the identified primary hits predicted residues that are essential for their binding in HSAT homologs from M. tuberculosis and S. aureus. ThermoFluor assay demonstrated direct binding of the identified primary hits with HSAT proteins. Few of the identified small molecules were able to inhibit growth of M. tuberculosis and S. aureus in liquid cultures. Taken together, our findings validated HSAT as an attractive target for development of new broad-spectrum anti-bacterial agents that should be effective against drug-resistant bacteria.
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Affiliation(s)
- Deepika Chaudhary
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India.,Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Avantika Singh
- Structural Biology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Mardiana Marzuki
- Infectious Diseases Labs (ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, 138648, Singapore
| | - Abhirupa Ghosh
- Division of Bioinformatics, Bose Institute, Kolkata, West Bengal, 700054, India
| | - Saqib Kidwai
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Tannu Priya Gosain
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Kiran Chawla
- Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Sonu Kumar Gupta
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Nisheeth Agarwal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Sudipto Saha
- Division of Bioinformatics, Bose Institute, Kolkata, West Bengal, 700054, India
| | - Yashwant Kumar
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Krishan Gopal Thakur
- Structural Biology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Amit Singhal
- Infectious Diseases Labs (ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, 138648, Singapore.,Singapore Immunology Network (SIgN), (A*STAR), Singapore, 138648, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Ramandeep Singh
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India. .,Tuberculosis Research Laboratory, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurugram Expressway, PO Box # 4, Faridabad, 121001, India.
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3
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Kuplińska A, Rząd K, Wojciechowski M, Milewski S, Gabriel I. Antifungal Effect of Penicillamine Due to the Selective Targeting of L-Homoserine O-Acetyltransferase. Int J Mol Sci 2022; 23:ijms23147763. [PMID: 35887110 PMCID: PMC9317633 DOI: 10.3390/ijms23147763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 11/16/2022] Open
Abstract
Due to the apparent similarity of fungal and mammalian metabolic pathways, the number of established antifungal targets is low, and the identification of novel ones is highly desirable. The results of our studies, presented in this work, indicate that the fungal biosynthetic pathway of L-methionine, an amino acid essential for humans, seems to be an attractive perspective. The MET2 gene from Candida albicans encoding L-homoserine O-acetyltransferase (CaMet2p), an enzyme catalyzing the first step in that pathway, was cloned and expressed as the native or the oligo-His-tagged fusion protein in Escherichia coli. The recombinant enzymes were purified and characterized for their basic molecular properties and substrate specificities. The purified MET2 gene product revealed the appropriate activity, catalyzed the conversion of L-homoserine (L-Hom) to O-acetyl-L-homoserine (OALH), and exhibited differential sensitivity to several L-Hom or OALH analogues, including penicillamine. Surprisingly, both penicillamine enantiomers (L- and D-Pen) displayed comparable inhibitory effects. The results of the docking of L- and D-Pen to the model of CaMet2p confirmed that both enantiomeric forms of the inhibitor are able to bind to the catalytic site of the enzyme with similar affinities and a similar binding mode. The sensitivity of some fungal cells to L-Pen, depending on the presence or absence of L-Met in the medium, clearly indicate Met2p targeting. Moreover, C. glabrata clinical strains that are resistant to fluconazole displayed a similar susceptibility to L-Pen as the wild-type strains. Our results prove the potential usefulness of Met2p as a molecular target for antifungal chemotherapy.
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Affiliation(s)
| | | | | | | | - Iwona Gabriel
- Correspondence: ; Tel.: +48-58-348-6078; Fax: +48-58-347-1144
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4
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Müller H, Terholsen H, Godehard SP, Badenhorst CPS, Bornscheuer UT. Recent Insights and Future Perspectives on Promiscuous Hydrolases/Acyltransferases. ACS Catal 2021. [DOI: 10.1021/acscatal.1c04543] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Henrik Müller
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
- Competence Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, 8820, Wädenswil, Switzerland
| | - Henrik Terholsen
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Simon P. Godehard
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Christoffel P. S. Badenhorst
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
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5
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Key amino acid residues in homoserine-acetyltransferase from M. tuberculosis give insight into the evolution of MetX family of enzymes - HAT, SAT and HST. Biochimie 2021; 189:13-25. [PMID: 34090964 DOI: 10.1016/j.biochi.2021.05.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/23/2021] [Accepted: 05/30/2021] [Indexed: 11/22/2022]
Abstract
Multiple sequence alignment of homoserine-acetyltransferases, serine-acetyltransferases and homoserine-succinyltransferases show they all belong to MetX family, having evolved from a common ancestor by conserving the catalytic site and substrate binding residues. The discrimination in the substrate selection arises due to the presence of substrate-specific residues lining the substrate-binding pocket. Mutation of Ala59 and Gly62 to Gly and Pro respectively in homoserine-acetyltransferase from M. tuberculosis resulted in a serine-acetyltransferase like enzyme as it acetylated both l-homoserine and l-serine. Homoserine-acetyltransferase from M. tuberculosis when mutated at positon 322 where Leu was converted to Arg, resulted in succinylation over acetylation of l-homoserine. Our studies establish the importance of the substrate binding residues in determining the type of activity possessed by MetX family, despite all of them having the same catalytic triad Ser-Asp-His. Hence key residues at the substrate binding pocket dictate whether the given enzyme shows predominant transferase or hydrolase activity.
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6
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MetA (Rv3341) from Mycobacterium tuberculosis H37Rv strain exhibits substrate dependent dual role of transferase and hydrolase activity. Biochimie 2020; 179:113-126. [PMID: 32976971 DOI: 10.1016/j.biochi.2020.09.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/10/2020] [Accepted: 09/13/2020] [Indexed: 02/08/2023]
Abstract
The metA (Rv3341) gene from Mycobacterium tuberculosis H37Rv strain encodes a homoserine-acetyltransferase (HAT) enzyme, also called MetA. This enzyme plays a key role in the biosynthetic pathway of methionine and is a potential target for the development of antimicrobial drugs. Purified MetA showed 40 kDa molecular mass on SDS-PAGE. Manual docking was performed with substrates acetyl-CoA, l-homoserine, and p-nitrophenylacetate using crystal structure coordinates of MetA (PDB ID 6PUX) from M. tuberculosis. Multiple sequence alignment indicated that catalytic triad residues Ser157, Asp320, His350 were conserved across species in acetyltransferases, esterases, and hydrolases. As a conserved pentapeptide, GXSMG belongs to α/β hydrolase superfamily and it shares similarity with esterases and hydrolases from different sources. Hydrolase activity of MetA was tested using (PNPA), N-acetylglycine, N-acetylmethionine and Phe-Gly as substrate. LC-MS confirmed that MetA possessed HAT activity, but no homoserine-succinyltransferase (HST) and serine-acetyltransferase (SAT) activities. Replacing acetyl-CoA with PNPA as acetyl group donor showed a drastic reduction in transferase activity, arising due to the interaction of R227 of the enzyme with PNPA. This could prevent the binding of the second substrate in the right orientation and results in the preferential transfer of the acetyl group to water, thus exhibiting hydrolase rather than transferase activity. In this paper, we report that MetA has both transferase and hydrolase activity depending on the correct orientation of the second substrate and the availability of the amino acids involved in enzyme-substrate interaction.
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7
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Fiebig T, Cramer JT, Bethe A, Baruch P, Curth U, Führing JI, Buettner FFR, Vogel U, Schubert M, Fedorov R, Mühlenhoff M. Structural and mechanistic basis of capsule O-acetylation in Neisseria meningitidis serogroup A. Nat Commun 2020; 11:4723. [PMID: 32948778 PMCID: PMC7501274 DOI: 10.1038/s41467-020-18464-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 08/20/2020] [Indexed: 02/08/2023] Open
Abstract
O-Acetylation of the capsular polysaccharide (CPS) of Neisseria meningitidis serogroup A (NmA) is critical for the induction of functional immune responses, making this modification mandatory for CPS-based anti-NmA vaccines. Using comprehensive NMR studies, we demonstrate that O-acetylation stabilizes the labile anomeric phosphodiester-linkages of the NmA-CPS and occurs in position C3 and C4 of the N-acetylmannosamine units due to enzymatic transfer and non-enzymatic ester migration, respectively. To shed light on the enzymatic transfer mechanism, we solved the crystal structure of the capsule O-acetyltransferase CsaC in its apo and acceptor-bound form and of the CsaC-H228A mutant as trapped acetyl-enzyme adduct in complex with CoA. Together with the results of a comprehensive mutagenesis study, the reported structures explain the strict regioselectivity of CsaC and provide insight into the catalytic mechanism, which relies on an unexpected Gln-extension of a classical Ser-His-Asp triad, embedded in an α/β-hydrolase fold.
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Affiliation(s)
- Timm Fiebig
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany.
| | | | - Andrea Bethe
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Petra Baruch
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Ute Curth
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Jana I Führing
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
- Fraunhofer International Consortium for Anti-Infective Research (iCAIR), Hannover, Germany
| | - Falk F R Buettner
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Ulrich Vogel
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Mario Schubert
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Roman Fedorov
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Martina Mühlenhoff
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany.
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8
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Azurmendi HF, Veeramachineni V, Freese S, Lichaa F, Freedberg DI, Vann WF. Chemical structure and genetic organization of the E. coli O6:K15 capsular polysaccharide. Sci Rep 2020; 10:12608. [PMID: 32724125 PMCID: PMC7387560 DOI: 10.1038/s41598-020-69476-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 07/13/2020] [Indexed: 12/20/2022] Open
Abstract
Capsular polysaccharides are important virulence factors in pathogenic bacteria. Characterizing the structural components and biosynthetic pathways for these polysaccharides is key to our ability to design vaccines and other preventative therapies that target encapsulated pathogens. Many gram-negative pathogens such as Neisseria meningitidis and Escherichia coli express acidic capsules. The E. coli K15 serotype has been identified as both an enterotoxigenic and uropathogenic pathogen. Despite its relevance as a disease-causing serotype, the associated capsular polysaccharide remains poorly characterized. We describe in this report the chemical structure of the K15 polysaccharide, based on chemical analysis and nuclear magnetic resonance (NMR) data. The repeating structure of the K15 polysaccharide consists of 4)-α-GlcpNAc-(1 → 5)-α-KDOp-(2 → partially O-acetylated at 3-hydroxyl of GlcNAc. We also report, the organization of the gene cluster responsible for capsule biosynthesis. We identify genes in this cluster that potentially encode an O-acetyltransferase, an N-acetylglucosamine transferase, and a KDO transferase consistent with the structure we report.
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Affiliation(s)
- Hugo F Azurmendi
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Vamsee Veeramachineni
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Stephen Freese
- Affinivax, 650 East Kendall St, Cambridge, MA, 02138, USA
| | - Flora Lichaa
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Darón I Freedberg
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Willie F Vann
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA.
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9
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Denesyuk A, Dimitriou PS, Johnson MS, Nakayama T, Denessiouk K. The acid-base-nucleophile catalytic triad in ABH-fold enzymes is coordinated by a set of structural elements. PLoS One 2020; 15:e0229376. [PMID: 32084230 PMCID: PMC7034887 DOI: 10.1371/journal.pone.0229376] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 02/05/2020] [Indexed: 01/09/2023] Open
Abstract
The alpha/beta-Hydrolases (ABH) are a structural class of proteins that are found widespread in nature and includes enzymes that can catalyze various reactions in different substrates. The catalytic versatility of the ABH fold enzymes, which has been a valuable property in protein engineering applications, is based on a similar acid-base-nucleophile catalytic mechanism. In our research, we are concerned with the structure that surrounds the key units of the catalytic machinery, and we have previously found conserved structural organizations that coordinate the catalytic acid, the catalytic nucleophile and the residues of the oxyanion hole. Here, we explore the architecture that surrounds the catalytic histidine at the active sites of enzymes from 40 ABH fold families, where we have identified six conserved interactions that coordinate the catalytic histidine next to the catalytic acid and the catalytic nucleophile. Specifically, the catalytic nucleophile is coordinated next to the catalytic histidine by two weak hydrogen bonds, while the catalytic acid is directly involved in the coordination of the catalytic histidine through by two weak hydrogen bonds. The imidazole ring of the catalytic histidine is coordinated by a CH-π contact and a hydrophobic interaction. Moreover, the catalytic triad residues are connected with a residue that is located at the core of the active site of ABH fold, which is suggested to be the fourth member of a “structural catalytic tetrad”. Besides their role in the stability of the catalytic mechanism, the conserved elements of the catalytic site are actively involved in ligand binding and affect other properties of the catalytic activity, such as substrate specificity, enantioselectivity, pH optimum and thermostability of ABH fold enzymes. These properties are regularly targeted in protein engineering applications, and thus, the identified conserved structural elements can serve as potential modification sites in order to develop ABH fold enzymes with altered activities.
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Affiliation(s)
- Alexander Denesyuk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, Russia
- * E-mail:
| | - Polytimi S. Dimitriou
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Mark S. Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Toru Nakayama
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi, Japan
| | - Konstantin Denessiouk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
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10
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Chaton CT, Rodriguez ES, Reed RW, Li J, Kenner CW, Korotkov KV. Structural analysis of mycobacterial homoserine transacetylases central to methionine biosynthesis reveals druggable active site. Sci Rep 2019; 9:20267. [PMID: 31889085 PMCID: PMC6937278 DOI: 10.1038/s41598-019-56722-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 12/16/2019] [Indexed: 01/14/2023] Open
Abstract
Mycobacterium tuberculosis is the cause of the world’s most deadly infectious disease. Efforts are underway to target the methionine biosynthesis pathway, as it is not part of the host metabolism. The homoserine transacetylase MetX converts l-homoserine to O-acetyl-l-homoserine at the committed step of this pathway. In order to facilitate structure-based drug design, we determined the high-resolution crystal structures of three MetX proteins, including M. tuberculosis (MtMetX), Mycolicibacterium abscessus (MaMetX), and Mycolicibacterium hassiacum (MhMetX). A comparison of homoserine transacetylases from other bacterial and fungal species reveals a high degree of structural conservation amongst the enzymes. Utilizing homologous structures with bound cofactors, we analyzed the potential ligandability of MetX. The deep active-site tunnel surrounding the catalytic serine yielded many consensus clusters during mapping, suggesting that MtMetX is highly druggable.
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Affiliation(s)
- Catherine T Chaton
- Department of Molecular & Cellular Biochemistry and the Center for Structural Biology, University of Kentucky, Lexington, KY, 40536, USA
| | - Emily S Rodriguez
- Department of Molecular & Cellular Biochemistry and the Center for Structural Biology, University of Kentucky, Lexington, KY, 40536, USA.,Department of Chemistry & Biochemistry, Ohio State University, Columbus, OH, 43210, USA
| | - Robert W Reed
- Department of Molecular & Cellular Biochemistry and the Center for Structural Biology, University of Kentucky, Lexington, KY, 40536, USA.,Division of Regulatory Services, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
| | - Jian Li
- Department of Molecular & Cellular Biochemistry and the Center for Structural Biology, University of Kentucky, Lexington, KY, 40536, USA.,Gannan Medical University, Ganzhou, Jiangxi, 341000, China
| | - Cameron W Kenner
- Department of Molecular & Cellular Biochemistry and the Center for Structural Biology, University of Kentucky, Lexington, KY, 40536, USA.,Georgetown College, Georgetown, KY, 40324, USA
| | - Konstantin V Korotkov
- Department of Molecular & Cellular Biochemistry and the Center for Structural Biology, University of Kentucky, Lexington, KY, 40536, USA.
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11
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Kruis AJ, Bohnenkamp AC, Patinios C, van Nuland YM, Levisson M, Mars AE, van den Berg C, Kengen SW, Weusthuis RA. Microbial production of short and medium chain esters: Enzymes, pathways, and applications. Biotechnol Adv 2019; 37:107407. [DOI: 10.1016/j.biotechadv.2019.06.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 05/24/2019] [Accepted: 06/09/2019] [Indexed: 12/12/2022]
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12
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Crystal structure and biochemical characterization of O-acetylhomoserine acetyltransferase from Mycobacterium smegmatis ATCC 19420. Biochem Biophys Res Commun 2019; 517:399-406. [PMID: 31378370 DOI: 10.1016/j.bbrc.2019.07.117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 07/29/2019] [Indexed: 11/24/2022]
Abstract
Mycobacterium smegmatis is a good model for studying the physiology and pathogenesis of Mycobacterium tuberculosis due to its genetic similarity. As methionine biosynthesis exists only in microorganisms, the enzymes involved in methionine biosynthesis can be a potential target for novel antibiotics. Homoserine O-acetyltransferase from M. smegmatis (MsHAT) catalyzes the transfer of acetyl-group from acetyl-CoA to homoserine. To investigate the molecular mechanism of MsHAT, we determined its crystal structure in apo-form and in complex with either CoA or homoserine and revealed the substrate binding mode of MsHAT. A structural comparison of MsHAT with other HATs suggests that the conformation of the α5 to α6 region might influence the shape of the dimer. In addition, the active site entrance shows an open or closed conformation and might determine the substrate binding affinity of HATs.
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13
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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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14
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Bastard K, Perret A, Mariage A, Bessonnet T, Pinet-Turpault A, Petit JL, Darii E, Bazire P, Vergne-Vaxelaire C, Brewee C, Debard A, Pellouin V, Besnard-Gonnet M, Artiguenave F, Médigue C, Vallenet D, Danchin A, Zaparucha A, Weissenbach J, Salanoubat M, de Berardinis V. Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis. Nat Chem Biol 2017; 13:858-866. [PMID: 28581482 DOI: 10.1038/nchembio.2397] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 03/22/2017] [Indexed: 12/30/2022]
Abstract
Experimental validation of enzyme function is crucial for genome interpretation, but it remains challenging because it cannot be scaled up to accommodate the constant accumulation of genome sequences. We tackled this issue for the MetA and MetX enzyme families, phylogenetically unrelated families of acyl-L-homoserine transferases involved in L-methionine biosynthesis. Members of these families are prone to incorrect annotation because MetX and MetA enzymes are assumed to always use acetyl-CoA and succinyl-CoA, respectively. We determined the enzymatic activities of 100 enzymes from diverse species, and interpreted the results by structural classification of active sites based on protein structure modeling. We predict that >60% of the 10,000 sequences from these families currently present in databases are incorrectly annotated, and suggest that acetyl-CoA was originally the sole substrate of these isofunctional enzymes, which evolved to use exclusively succinyl-CoA in the most recent bacteria. We also uncovered a divergent subgroup of MetX enzymes in fungi that participate only in L-cysteine biosynthesis as O-succinyl-L-serine transferases.
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Affiliation(s)
- Karine Bastard
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Alain Perret
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Aline Mariage
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Thomas Bessonnet
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Agnès Pinet-Turpault
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Jean-Louis Petit
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Ekaterina Darii
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Pascal Bazire
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Carine Vergne-Vaxelaire
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Clémence Brewee
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Adrien Debard
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Virginie Pellouin
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Marielle Besnard-Gonnet
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | | | - Claudine Médigue
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - David Vallenet
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Antoine Danchin
- Institute of Cardiometabolism and Nutrition (ICAN), Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Anne Zaparucha
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Jean Weissenbach
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Marcel Salanoubat
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Véronique de Berardinis
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
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15
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A Novel Subfamily Esterase with a Homoserine Transacetylase-like Fold but No Transferase Activity. Appl Environ Microbiol 2017; 83:AEM.00131-17. [PMID: 28235874 DOI: 10.1128/aem.00131-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 02/16/2017] [Indexed: 02/02/2023] Open
Abstract
Microbial esterases play important roles in deep-sea organic carbon degradation and cycling. Although they have similar catalytic triads and oxyanion holes, esterases are hydrolases and homoserine transacetylases (HTAs) are transferases. Because two HTA homologs were identified as acetyl esterases, the HTA family was recently divided into the bona fide acetyltransferase subfamily and the acetyl esterase subfamily. Here, we identified and characterized a novel HTA-like esterase, Est22, from a deep-sea sedimentary metagenomic library. Est22 could efficiently hydrolyze esters with acyl lengths of up to six carbon atoms but had no transacetylase activity, which is different from HTAs and HTA-like acetyl esterases. Phylogenetic analysis also showed that Est22 and its homologs form a separate branch of the HTA family. We solved the structures of Est22 and its L374D mutant and modeled the structure of the L374D mutant with p-nitrophenyl butyrate. Based on structural, mutational, and biochemical analyses, Phe71 and Met176 in the oxyanion hole and Arg294 were revealed to be the key substrate-binding residues. A detailed structural comparison indicated that differences in their catalytic tunnels lead to the different substrate specificities of Est22 and the other two HTA subfamilies. Biochemical and sequence analyses suggested that Est22 homologs may have the same substrate recognition and catalysis mechanisms as Est22. Due to the significant differences in sequences, structures, and substrate specificities between Est22 (and its homologs) and the other two HTA subfamilies, we suggest that Est22 and its homologs represent a new subfamily in the HTA family.IMPORTANCE Microbial esterases play important roles in the turnover of organic carbon in the deep sea. Esterases and HTAs represent two groups of α/β hydrolases. Esterases catalyze the hydrolysis of simple esters and are widely used in the pharmaceutical and agrochemical industries, while HTAs catalyze the transfer of an acetyl group from acetyl-coenzyme A (CoA) to homoserine and are essential for microbial growth. Here, we report on a novel HTA-like esterase, Est22, from a deep-sea sediment. Because of the significant differences in sequences, structures, and substrate specificities of HTAs and HTA-like acetyl esterases, Est22 and its homologs represent a new subfamily in the HTA family. This study offers new knowledge regarding marine esterases.
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16
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Shim J, Shin Y, Lee I, Kim SY. l-Methionine Production. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 159:153-177. [DOI: 10.1007/10_2016_30] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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17
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Tölzer C, Pal S, Watzlawick H, Altenbuchner J, Niefind K. A novel esterase subfamily with α/β-hydrolase fold suggested by structures of two bacterial enzymes homologous to L-homoserine O-acetyl transferases. FEBS Lett 2015; 590:174-84. [PMID: 26787467 DOI: 10.1002/1873-3468.12031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 11/25/2015] [Accepted: 11/26/2015] [Indexed: 11/09/2022]
Abstract
MekB from Pseudomonas veronii and CgHle from Corynebacteriumglutamicum belong to the superfamily of α/β-hydrolase fold proteins. Based on sequence comparisons, they are annotated as homoserine transacetylases in popular databases like UNIPROT, PFAM or ESTHER. However, experimentally, MekB and CgHle were shown to be esterases that hydrolyse preferentially acetic acid esters. We describe the x-ray structures of these enzymes solved to high resolution. The overall structures confirm the close relatedness to experimentally validated homoserine acetyl transferases, but simultaneously the structures exclude the ability of MekB and CgHle to bind homoserine and acetyl-CoA. Insofar the MekB and CgHle structures suggest dividing the homoserine transacetylase family into subfamilies, namely genuine acetyl transferases and acetyl esterases with MekB and CgHle as constituting members of the latter.
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Affiliation(s)
- Christine Tölzer
- Department für Chemie, Institut für Biochemie, Universität zu Köln, Germany
| | - Sonia Pal
- Department für Chemie, Institut für Biochemie, Universität zu Köln, Germany
| | | | | | - Karsten Niefind
- Department für Chemie, Institut für Biochemie, Universität zu Köln, Germany
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18
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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: 177] [Impact Index Per Article: 19.7] [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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19
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Thangavelu B, Pavlovsky AG, Viola R. Structure of homoserine O-acetyltransferase from Staphylococcus aureus: the first Gram-positive ortholog structure. Acta Crystallogr F Struct Biol Commun 2014; 70:1340-5. [PMID: 25286936 PMCID: PMC4188076 DOI: 10.1107/s2053230x14018664] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 08/18/2014] [Indexed: 11/10/2022] Open
Abstract
Homoserine O-acetyltransferase (HTA) catalyzes the formation of L-O-acetyl-homoserine from L-homoserine through the transfer of an acetyl group from acetyl-CoA. This is the first committed step required for the biosynthesis of methionine in many fungi, Gram-positive bacteria and some Gram-negative bacteria. The structure of HTA from Staphylococcus aureus (SaHTA) has been determined to a resolution of 2.45 Å. The structure belongs to the α/β-hydrolase superfamily, consisting of two distinct domains: a core α/β-domain containing the catalytic site and a lid domain assembled into a helical bundle. The active site consists of a classical catalytic triad located at the end of a deep tunnel. Structure analysis revealed some important differences for SaHTA compared with the few known structures of HTA.
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Affiliation(s)
- Bharani Thangavelu
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo, OH 43606, USA
| | - Alexander G. Pavlovsky
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo, OH 43606, USA
| | - Ronald Viola
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo, OH 43606, USA
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20
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Moynihan PJ, Clarke AJ. Mechanism of action of peptidoglycan O-acetyltransferase B involves a Ser-His-Asp catalytic triad. Biochemistry 2014; 53:6243-51. [PMID: 25215566 DOI: 10.1021/bi501002d] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The O-acetylation of the essential cell wall polymer peptidoglycan is essential in many bacteria for their integrity and survival, and it is catalyzed by peptidoglycan O-acetlytransferase B (PatB). Using PatB from Neisseria gonorrhoeae as the model, we have shown previously that the enzyme has specificity for polymeric muropeptides that possess tri- and tetrapeptide stems and that rates of reaction increase with increasing degrees of polymerization. Here, we present the catalytic mechanism of action of PatB, the first to be described for an O-acetyltransferase of any bacterial exopolysaccharide. The influence of pH on PatB activity was investigated, and pKa values of 6.4-6.45 and 6.25-6.35 for the enzyme-substrate complex (kcat vs pH) and the free enzyme (kcat·KM(-1) vs pH), respectively, were determined for the respective cosubstrates. The enzyme is partially inactivated by sulfonyl fluorides but not by EDTA, suggesting the participation of a serine residue in its catalytic mechanism. Alignment of the known and hypothetical PatB amino acid sequences identified Ser133, Asp302, and His305 as three invariant amino acid residues that could potentially serve as a catalytic triad. Replacement of Asp302 with Ala resulted in an enzyme with less than 20% residual activity, whereas activity was barely detectable with (His305 → Ala)PatB and (Ser133 → Ala)PatB was totally inactive. The reaction intermediate of the transferase reaction involving acetyl- and propionyl-acyl donors was trapped on both the wild-type and (Asp302 → Ala) enzymes and LC-MS/MS analysis of tryptic peptides identified Ser133 as the catalytic nucleophile. A transacetylase mechanism is proposed based on the mechanism of action of serine esterases.
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Affiliation(s)
- Patrick J Moynihan
- Department of Molecular and Cellular Biology, University of Guelph , Guelph, Ontario N1G 2W1 Canada
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21
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Huang C, Roncoroni M, Gardner RC. MET2 affects production of hydrogen sulfide during wine fermentation. Appl Microbiol Biotechnol 2014; 98:7125-35. [PMID: 24841117 DOI: 10.1007/s00253-014-5789-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 04/10/2014] [Accepted: 04/13/2014] [Indexed: 01/08/2023]
Abstract
The production of hydrogen sulfide (H2S) during yeast fermentation contributes negatively to wine aroma. We have mapped naturally occurring mutations in commercial wine strains that affect production of H2S. A dominant R310G mutant allele of MET2, which encodes homoserine O-acetyltransferase, is present in several wine yeast strains as well as in the main lab strain S288c. Reciprocal hemizygosity and allele swap experiments demonstrated that the MET2 R310G allele confers reduced H2S production. Mutations were also identified in genes encoding the two subunits of sulfite reductase, MET5 and MET10, which were associated with reduced H2S production. The most severe of these, an allele of MET10, showed five additional phenotypes: reduced growth rate on sulfate, elevated secretion of sulfite, and reduced production in wine of three volatile sulfur compounds: methionol, carbon disulfide and methylthioacetate. Alleles of MET5 and MET10, but not MET2, affected H2S production measured by colour assays on BiGGY indicator agar, but MET2 effects were seen when bismuth was added to agar plates made with Sauvignon blanc grape juice. Collectively, the data are consistent with the hypothesis that H2S production during wine fermentation results predominantly from enzyme activity in the sulfur assimilation pathway. Lower H2S production results from mutations that reduce the activity of sulfite reductase, the enzyme that produces H2S, or that increase the activity of L-homoserine-O-acetyltransferase, which produces substrate for the next step in the sulfur assimilation pathway.
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Affiliation(s)
- Chien Huang
- Wine Science Group, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
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22
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Crystallographic study to determine the substrate specificity of an L-serine-acetylating enzyme found in the D-cycloserine biosynthetic pathway. J Bacteriol 2013; 195:1741-9. [PMID: 23396912 DOI: 10.1128/jb.02085-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
DcsE, one of the enzymes found in the d-cycloserine biosynthetic pathway, displays a high sequence homology to l-homoserine O-acetyltransferase (HAT), but it prefers l-serine over l-homoserine as the substrate. To clarify the substrate specificity, in the present study we determined the crystal structure of DcsE at a 1.81-Å resolution, showing that the overall structure of DcsE is similar to that of HAT, whereas a turn region to form an oxyanion hole is obviously different between DcsE and HAT: in detail, the first and last residues in the turn of DcsE are Gly(52) and Pro(55), respectively, but those of HAT are Ala and Gly, respectively. In addition, more water molecules were laid on one side of the turn region of DcsE than on that of HAT, and a robust hydrogen-bonding network was formed only in DcsE. We created a HAT-like mutant of DcsE in which Gly(52) and Pro(55) were replaced by Ala and Gly, respectively, showing that the mutant acetylates l-homoserine but scarcely acetylates l-serine. The crystal structure of the mutant DcsE shows that the active site, including the turn and its surrounding waters, is similar to that of HAT. These findings suggest that a methyl group of the first residue in the turn of HAT plays a role in excluding the binding of l-serine to the substrate-binding pocket. In contrast, the side chain of the last residue in the turn of DcsE may need to form an extensive hydrogen-bonding network on the turn, which interferes with the binding of l-homoserine.
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23
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De Pascale G, Griffiths EJ, Shakya T, Nazi I, Wright GD. Identification and Characterization of New Inhibitors of Fungal Homoserine Kinase. Chembiochem 2011; 12:1179-82. [DOI: 10.1002/cbic.201100121] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2011] [Indexed: 11/09/2022]
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24
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De Pascale G, Nazi I, Harrison PHM, Wright GD. β-Lactone natural products and derivatives inactivate homoserine transacetylase, a target for antimicrobial agents. J Antibiot (Tokyo) 2011; 64:483-7. [DOI: 10.1038/ja.2011.37] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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25
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Jiang Y, Morley KL, Schrag JD, Kazlauskas RJ. Different active-site loop orientation in serine hydrolases versus acyltransferases. Chembiochem 2011; 12:768-76. [PMID: 21351219 DOI: 10.1002/cbic.201000693] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Indexed: 11/07/2022]
Abstract
Acyl transfer is a key reaction in biosynthesis, including synthesis of antibiotics and polyesters. Although researchers have long recognized the similar protein fold and catalytic machinery in acyltransferases and hydrolases, the molecular basis for the different reactivity has been a long-standing mystery. By comparison of X-ray structures, we identified a different oxyanion-loop orientation in the active site. In esterases/lipases a carbonyl oxygen points toward the active site, whereas in acyltransferases a NH of the main-chain amide points toward the active site. Amino acid sequence comparisons alone cannot identify such a difference in the main-chain orientation. To identify how this difference might change the reaction mechanism, we solved the X-ray crystal structure of Pseudomonas fluorescens esterase containing a sulfonate transition-state analogue bound to the active-site serine. This structure mimics the transition state for the attack of water on the acyl-enzyme and shows a bridging water molecule between the carbonyl oxygen mentioned above and the sulfonyl oxygen that mimics the attacking water. A possible mechanistic role for this bridging water molecule is to position and activate the attacking water molecule in hydrolases, but to deactivate the attacking water molecule in acyl transferases.
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Affiliation(s)
- Yun Jiang
- Department of Biochemistry, Molecular Biology and Biophysics, Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
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26
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Johnston JM, Jiang M, Guo Z, Baker EN. Structural and functional analysis of Rv0554 from Mycobacterium tuberculosis: testing a putative role in menaquinone biosynthesis. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:909-17. [PMID: 20693690 DOI: 10.1107/s0907444910025771] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Accepted: 06/30/2010] [Indexed: 05/26/2023]
Abstract
Mycobacterium tuberculosis, the cause of tuberculosis, is a devastating human pathogen against which new drugs are urgently needed. Enzymes from the biosynthetic pathway for menaquinone are considered to be valid drug targets. The protein encoded by the open reading frame Rv0554 has been expressed, purified and subjected to structural and functional analysis to test for a putative role in menaquinone biosynthesis. The crystal structure of Rv0554 has been solved and refined in two different space groups at 2.35 and 1.9 A resolution. The protein is dimeric, with an alpha/beta-hydrolase monomer fold. In each monomer, a large cavity adjacent to the catalytic triad is enclosed by a helical lid. Dimerization is mediated by the lid regions. Small-molecule additives used in crystallization bind in the active site, but no binding of ligands related to menaquinone biosynthesis could be detected and functional assays failed to support possible roles in menaquinone biosynthesis.
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Affiliation(s)
- Jodie M Johnston
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
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27
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Moynihan PJ, Clarke AJ. O-acetylation of peptidoglycan in gram-negative bacteria: identification and characterization of peptidoglycan O-acetyltransferase in Neisseria gonorrhoeae. J Biol Chem 2010; 285:13264-73. [PMID: 20178982 DOI: 10.1074/jbc.m110.107086] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ape2 gene encoding a hypothetical O-acetylpeptidoglycan esterase was amplified from genomic DNA of Neisseria gonorrhoeae FA1090 and cloned to encode either the full-length protein or a truncated version lacking its hypothetical signal sequence. Expression trials revealed that production of the full-length version possessing either an N-terminal or C-terminal His(6) tag was toxic to Escherichia coli transformants and that the host rapidly degraded the small amount of protein that was produced. An N-terminally truncated protein could be produced in sufficient yields for purification only if it possessed an N-terminal His(6) tag. This form of the protein was isolated and purified to apparent homogeneity, and its enzymatic properties were characterized. Whereas the protein could bind to insoluble peptidoglycan, it did not function as an esterase. Phenotypic characterization of E. coli transformants producing various forms of the protein revealed that it functions instead to O-acetylate peptidoglycan within the periplasm, and it was thus renamed peptidoglycan O-acetyltransferase B. This activity was found to be dependent upon a second protein, which functions to translocate acetate from the cytoplasm to the periplasm, demonstrating that the O-acetylation of peptidoglycan in N. gonorrhoeae, and other gram-negative bacteria, requires a two component system.
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Affiliation(s)
- Patrick J Moynihan
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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28
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Max D, Hesse M, Volkmer I, Staege MS. High expression of the evolutionarily conserved alpha/beta hydrolase domain containing 6 (ABHD6) in Ewing tumors. Cancer Sci 2009; 100:2383-9. [PMID: 19793082 PMCID: PMC11158961 DOI: 10.1111/j.1349-7006.2009.01347.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Despite improvements in the treatment of patients with Ewing family tumors (EFT), the prognosis for patients with advanced disease is still unsatisfactory. Recently, we identified lipase I as an EFT-associated gene that might be interesting for the development of new immunological or pharmacological treatment strategies. Lipase I is a member of the large protein superfamilies of alpha/beta hydrolases and serine hydrolases. In the present paper we describe high expression of another member of these superfamilies in EFT. By DNA microarray data base mining we found exceptional high expression of alpha/beta hydrolase domain containing 6 (ABHD6) in EFT but not in other sarcomas. Expression of ABHD6 in EFT correlated with expression of another EFT-associated gene, aristaless. Analysis of ABHD6-associated GGAA microsatellites revealed shorter microsatellites in EFT with lack of ABHD6 expression. ABHD6 homologues were found in varying chordata but not in other animal species. Based on homology modeling we predicted the 3D-structure of ABHD6, which shows high similarity with bacterial homoserine transacetylases. High expression of ABHD6 in EFT in comparison to normal tissues and other tumors suggests that ABHD6 might be an interesting new diagnostic or therapeutic target for EFT. However, knock down of ABHD6 in EFT cells did not inhibit tumor cell growth.
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Affiliation(s)
- Daniela Max
- Children's Cancer Research Center, Martin-Luther-University Halle-Wittenberg, University Clinic and Polyclinic for Child and Adolescent Medicine, Halle, Germany
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Tölzer C, Pal S, Watzlawick H, Altenbuchner J, Niefind K. Crystallization and preliminary crystallographic analysis of cgHle, a homoserine acetyltransferase homologue, from Corynebacterium glutamicum. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:34-8. [PMID: 19153452 PMCID: PMC2628851 DOI: 10.1107/s1744309108039146] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2008] [Accepted: 11/21/2008] [Indexed: 11/10/2022]
Abstract
CgHle is an enzyme that is encoded by gene cg0961 from Corynebacterium glutamicum. The physiological function of cgHle is so far unclear. Bioinformatic annotations based on sequence homology indicated that cgHle may be an acetyl-CoA:homoserine acetyl transferase and as such may be involved in methionine biosynthesis, but recent evidence has shown that it is an esterase that catalyzes the hydrolysis of acetyl esters. Here, the crystallization of cgHle in two orthorhombic crystal forms, a trigonal crystal form and a monoclinic crystal form is described. The trigonal crystals have a solvent content of 83.7%, which is one of the highest solvent contents ever found for protein crystals. One of the orthorhombic crystals diffracted X-rays to at least 1.2 A resolution.
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Affiliation(s)
- Christine Tölzer
- Universität zu Köln, Department für Chemie, Institut für Biochemie, Zülpicher Strasse 47, D-50674 Köln, Germany
| | - Sonia Pal
- Universität zu Köln, Department für Chemie, Institut für Biochemie, Zülpicher Strasse 47, D-50674 Köln, Germany
| | - Hildegard Watzlawick
- Universität Stuttgart, Institut für Industrielle Genetik, Allmandring 31, D-70569 Stuttgart, Germany
| | - Josef Altenbuchner
- Universität Stuttgart, Institut für Industrielle Genetik, Allmandring 31, D-70569 Stuttgart, Germany
| | - Karsten Niefind
- Universität zu Köln, Department für Chemie, Institut für Biochemie, Zülpicher Strasse 47, D-50674 Köln, Germany
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Elford TG, Ulaczyk-Lesanko A, De Pascale G, Wright GD, Hall DG. Diversity-Oriented Synthesis and Preliminary Biological Screening of Highly Substituted Five-Membered Lactones and Lactams Originating From an Allyboration of Aldehydes and Imines. ACTA ACUST UNITED AC 2008; 11:155-68. [DOI: 10.1021/cc8001487] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tim G. Elford
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2, and M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada, L8N 3Z5
| | - Agnieszka Ulaczyk-Lesanko
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2, and M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada, L8N 3Z5
| | - Gianfranco De Pascale
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2, and M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada, L8N 3Z5
| | - Gerard D. Wright
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2, and M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada, L8N 3Z5
| | - Dennis G. Hall
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2, and M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada, L8N 3Z5
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Bergfeld AK, Claus H, Lorenzen NK, Spielmann F, Vogel U, Mu Hlenhoff M. The polysialic acid-specific O-acetyltransferase OatC from Neisseria meningitidis serogroup C evolved apart from other bacterial sialate O-acetyltransferases. J Biol Chem 2008; 284:6-16. [PMID: 18986988 DOI: 10.1074/jbc.m807518200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Neisseria meningitidis serogroup C is a major cause of bacterial meningitis and septicaemia. This human pathogen is protected by a capsule composed of alpha2,9-linked polysialic acid that represents an important virulence factor. In the majority of strains, the capsular polysaccharide is modified by O-acetylation at C-7 or C-8 of the sialic acid residues. The gene encoding the capsule modifying O-acetyltransferase is part of the capsule gene complex and shares no sequence similarities with other proteins. Here, we describe the purification and biochemical characterization of recombinant OatC. The enzyme was found as a homodimer, with the first 34 amino acids forming an efficient oligomerization domain that worked even in a different protein context. Using acetyl-CoA as donor substrate, OatC transferred acetyl groups exclusively onto polysialic acid joined by alpha2,9-linkages and did not act on free or CMP-activated sialic acid. Motif scanning revealed a nucleophile elbow motif (GXS286XGG), which is a hallmark of alpha/beta-hydrolase fold enzymes. In a comprehensive site-directed mutagenesis study, we identified a catalytic triad composed of Ser-286, Asp-376, and His-399. Consistent with a double-displacement mechanism common to alpha/beta-hydrolase fold enzymes, a covalent acetylenzyme intermediate was found. Together with secondary structure prediction highlighting an alpha/beta-hydrolase fold topology, our data provide strong evidence that OatC belongs to the alpha/beta-hydrolase fold family. This clearly distinguishes OatC from all other bacterial sialate O-acetyltransferases known so far because these are members of the hexapeptide repeat family, a class of acyltransferases that adopt a left-handed beta-helix fold and assemble into catalytic trimers.
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Affiliation(s)
- Anne K Bergfeld
- Department of Cellular Chemistry, Medical School Hannover, 30623 Hannover, Germany and the Institute for Hygiene and Microbiology, University of Wu¨rzburg, 97080 Wu¨rzburg, Germany
| | - Heike Claus
- Department of Cellular Chemistry, Medical School Hannover, 30623 Hannover, Germany and the Institute for Hygiene and Microbiology, University of Wu¨rzburg, 97080 Wu¨rzburg, Germany
| | - Nina K Lorenzen
- Department of Cellular Chemistry, Medical School Hannover, 30623 Hannover, Germany and the Institute for Hygiene and Microbiology, University of Wu¨rzburg, 97080 Wu¨rzburg, Germany
| | - Fabian Spielmann
- Department of Cellular Chemistry, Medical School Hannover, 30623 Hannover, Germany and the Institute for Hygiene and Microbiology, University of Wu¨rzburg, 97080 Wu¨rzburg, Germany
| | - Ulrich Vogel
- Department of Cellular Chemistry, Medical School Hannover, 30623 Hannover, Germany and the Institute for Hygiene and Microbiology, University of Wu¨rzburg, 97080 Wu¨rzburg, Germany
| | - Martina Mu Hlenhoff
- Department of Cellular Chemistry, Medical School Hannover, 30623 Hannover, Germany and the Institute for Hygiene and Microbiology, University of Wu¨rzburg, 97080 Wu¨rzburg, Germany.
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Dherbécourt J, Falentin H, Canaan S, Thierry A. A genomic search approach to identify esterases in Propionibacterium freudenreichii involved in the formation of flavour in Emmental cheese. Microb Cell Fact 2008; 7:16. [PMID: 18498642 PMCID: PMC2442053 DOI: 10.1186/1475-2859-7-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2008] [Accepted: 05/22/2008] [Indexed: 11/25/2022] Open
Abstract
Background Lipolysis is an important process of cheese ripening that contributes to the formation of flavour. Propionibacterium freudenreichii is the main agent of lipolysis in Emmental cheese; however, the enzymes involved produced by this species have not yet been identified. Lipolysis is performed by esterases (carboxylic ester hydrolases, EC 3.1.1.-) which are able to hydrolyse acylglycerols bearing short, medium and long chain fatty acids. The genome sequence of P. freudenreichii type strain CIP103027T was recently obtained in our laboratory. The aim of this study was to identify as exhaustively as possible the potential esterases in P. freudenreichii that could be involved in the hydrolysis of acylglycerols in Emmental cheese. The proteins identified were produced in a soluble and active form by heterologous expression in Escherichia coli for further study of their activity and specificity of hydrolysed substrates. Results The approach chosen was a genomic search approach that combined and compared four methods based on automatic and manual searches of homology and motifs among P. freudenreichii CIP103027T predicted proteins. Twenty-three putative esterases were identified in this step. Then a selection step permitted to focus the study on the 12 most probable esterases, according to the presence of the GXSXG motif of the α/β hydrolase fold family. The 12 corresponding coding sequences were cloned in expression vectors, containing soluble N-terminal fusion proteins. The best conditions to express each protein in a soluble form were found thanks to an expression screening, using an incomplete factorial experimental design. Eleven out of the 12 proteins were expressed in a soluble form in E. coli and six showed esterase activity on 1-naphthyl acetate and/or propionate, as demonstrated by a zymographic method. Conclusion We were able to demonstrate that our genomic search approach was efficient to identify esterases from the genome of a P. freudenreichii strain, more exhaustively than classical approaches. This study highlights the interest in using the automatic search of motifs, with the manual search of homology to previously characterised enzymes as a complementary method. Only further characterisations would permit the identification of the esterases of P. freudenreichii involved in the lipolysis in Emmental cheese.
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Affiliation(s)
- Julien Dherbécourt
- INRA, Agrocampus Rennes, UMR1253 Science et Technologie du Lait et de l'OEuf, F-35000 Rennes, France.
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Lejon S, Ellis J, Valegård K. The Last Step in Cephalosporin C Formation Revealed: Crystal Structures of Deacetylcephalosporin C Acetyltransferase from Acremonium chrysogenum in Complexes with Reaction Intermediates. J Mol Biol 2008; 377:935-44. [DOI: 10.1016/j.jmb.2008.01.047] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2007] [Revised: 01/04/2008] [Accepted: 01/18/2008] [Indexed: 11/24/2022]
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Curien G, Biou V, Mas-Droux C, Robert-Genthon M, Ferrer JL, Dumas R. Amino acid biosynthesis: new architectures in allosteric enzymes. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2008; 46:325-339. [PMID: 18272376 DOI: 10.1016/j.plaphy.2007.12.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2007] [Indexed: 05/25/2023]
Abstract
This review focuses on the allosteric controls in the Aspartate-derived and the branched-chain amino acid biosynthetic pathways examined both from kinetic and structural points of view. The objective is to show the differences that exist among the plant and microbial worlds concerning the allosteric regulation of these pathways and to unveil the structural bases of this diversity. Indeed, crystallographic structures of enzymes from these pathways have been determined in bacteria, fungi and plants, providing a wonderful opportunity to obtain insight into the acquisition and modulation of allosteric controls in the course of evolution. This will be examined using two enzymes, threonine synthase and the ACT domain containing enzyme aspartate kinase. In a last part, as many enzymes in these pathways display regulatory domains containing the conserved ACT module, the organization of ACT domains in this kind of allosteric enzymes will be reviewed, providing explanations for the variety of allosteric effectors and type of controls observed.
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Affiliation(s)
- Gilles Curien
- Laboratoire de Physiologie Cellulaire Végétale, Université Joseph Fourier, Commissariat à l'Energie Atomique, Institut de Recherche et de Technologie des Sciences du Vivant, 38054 Grenoble, France
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Zubieta C, Arkus KAJ, Cahoon RE, Jez JM. A single amino acid change is responsible for evolution of acyltransferase specificity in bacterial methionine biosynthesis. J Biol Chem 2008; 283:7561-7. [PMID: 18216013 DOI: 10.1074/jbc.m709283200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacteria and yeast rely on either homoserine transsuccinylase (HTS, metA) or homoserine transacetylase (HTA; met2) for the biosynthesis of methionine. Although HTS and HTA catalyze similar chemical reactions, these proteins are typically unrelated in both sequence and three-dimensional structure. Here we present the 2.0 A resolution x-ray crystal structure of the Bacillus cereus metA protein in complex with homoserine, which provides the first view of a ligand bound to either HTA or HTS. Surprisingly, functional analysis of the B. cereus metA protein shows that it does not use succinyl-CoA as a substrate. Instead, the protein catalyzes the transacetylation of homoserine using acetyl-CoA. Therefore, the B. cereus metA protein functions as an HTA despite greater than 50% sequence identity with bona fide HTS proteins. This result emphasizes the need for functional confirmation of annotations of enzyme function based on either sequence or structural comparisons. Kinetic analysis of site-directed mutants reveals that the B. cereus metA protein and the E. coli HTS share a common catalytic mechanism. Structural and functional examination of the B. cereus metA protein reveals that a single amino acid in the active site determines acetyl-CoA (Glu-111) versus succinyl-CoA (Gly-111) specificity in the metA-like of acyltransferases. Switching of this residue provides a mechanism for evolving substrate specificity in bacterial methionine biosynthesis. Within this enzyme family, HTS and HTA activity likely arises from divergent evolution in a common structural scaffold with conserved catalytic machinery and homoserine binding sites.
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Affiliation(s)
- Chloe Zubieta
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
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36
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Park SY, Lee SH, Lee J, Nishi K, Kim YS, Jung CH, Kim JS. High-resolution structure of ybfF from Escherichia coli K12: a unique substrate-binding crevice generated by domain arrangement. J Mol Biol 2008; 376:1426-37. [PMID: 18215690 DOI: 10.1016/j.jmb.2007.12.062] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2007] [Revised: 12/08/2007] [Accepted: 12/23/2007] [Indexed: 11/30/2022]
Abstract
Esterases are one of the most common enzymes and are involved in diverse cellular functions. ybfF protein from Escherichia coli (Ec_ybfF) belongs to the esterase family for the large substrates, palmitoyl coenzyme A and malonyl coenzyme A, which are important cellular intermediates for energy conversion and biomolecular synthesis. To obtain molecular information on ybfF esterase, which is found in a wide range of microorganisms, we elucidated the crystal structures of Ec_ybfF in complexes with small molecules at resolutions of 1.1 and 1.68 A, respectively. The structure of Ec_ybfF is composed of a globular alpha/beta hydrolase domain with a three-helical bundle cap, which is linked by a kinked helix to the alpha/beta hydrolase domain. It contains a catalytic tetrad of Ser-His-Asp-Ser with the first Ser acting as a nucleophile. The unique spatial arrangement and orientation of the helical cap with respect to the alpha/beta hydrolase domain form a substrate-binding crevice for large substrates. The helical cap is also directly involved in catalysis by providing a substrate anchor, viz., the conserved residues of Arg123 and Tyr208. The high-resolution structure of Ec_ybfF shows that the inserted helical bundle structure and its spatial orientation with respect to the alpha/beta hydrolase domain are critical for creating a large inner space and constituting a specific active site, thereby providing the broad substrate spectrum toward large biomolecules.
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Affiliation(s)
- Suk-Youl Park
- Department of Chemistry and Institute of Basic Sciences, Chonnam National University, 300 Yongbong-dong, Buk-gu, Gwangju 500-757, Korea
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Wang M, Liu L, Wang Y, Wei Z, Zhang P, Li Y, Jiang X, Xu H, Gong W. Crystal structure of homoserine O-acetyltransferase from Leptospira interrogans. Biochem Biophys Res Commun 2007; 363:1050-6. [DOI: 10.1016/j.bbrc.2007.08.153] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2007] [Accepted: 08/23/2007] [Indexed: 10/22/2022]
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Zubieta C, Krishna SS, McMullan D, Miller MD, Abdubek P, Agarwalla S, Ambing E, Astakhova T, Axelrod HL, Carlton D, Chiu HJ, Clayton T, Deller M, DiDonato M, Duan L, Elsliger MA, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Kumar A, Marciano D, Morse AT, Nigoghossian E, Oommachen S, Reyes R, Rife CL, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structure of homoserine O-succinyltransferase from Bacillus cereus at 2.4 Å resolution. Proteins 2007; 68:999-1005. [PMID: 17546672 DOI: 10.1002/prot.21208] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Chloe Zubieta
- Joint Center for Structural Genomics, Stanford University, Menlo Park, California, USA
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