1
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Bennett JM, Narwal SK, Kabeche S, Abegg D, Thathy V, Hackett F, Yeo T, Li VL, Muir R, Faucher F, Lovell S, Blackman MJ, Adibekian A, Yeh E, Fidock DA, Bogyo M. Mixed alkyl/aryl phosphonates identify metabolic serine hydrolases as antimalarial targets. Cell Chem Biol 2024; 31:1714-1728.e10. [PMID: 39137783 DOI: 10.1016/j.chembiol.2024.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 06/20/2024] [Accepted: 07/15/2024] [Indexed: 08/15/2024]
Abstract
Malaria, caused by Plasmodium falciparum, remains a significant health burden. One major barrier for developing antimalarial drugs is the ability of the parasite to rapidly generate resistance. We previously demonstrated that salinipostin A (SalA), a natural product, potently kills parasites by inhibiting multiple lipid metabolizing serine hydrolases, a mechanism that results in a low propensity for resistance. Given the difficulty of employing natural products as therapeutic agents, we synthesized a small library of lipidic mixed alkyl/aryl phosphonates as bioisosteres of SalA. Two constitutional isomers exhibited divergent antiparasitic potencies that enabled the identification of therapeutically relevant targets. The active compound kills parasites through a mechanism that is distinct from both SalA and the pan-lipase inhibitor orlistat and shows synergistic killing with orlistat. Our compound induces only weak resistance, attributable to mutations in a single protein involved in multidrug resistance. These data suggest that mixed alkyl/aryl phosphonates are promising, synthetically tractable antimalarials.
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Affiliation(s)
- John M Bennett
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Sunil K Narwal
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA; Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, USA
| | - Stephanie Kabeche
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Abegg
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | - Vandana Thathy
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA; Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, USA
| | - Fiona Hackett
- Malaria Biochemistry Laboratory, Francis Crick Institute, London NW1 1AT, UK
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA; Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, USA
| | - Veronica L Li
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Ryan Muir
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Franco Faucher
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Scott Lovell
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael J Blackman
- Malaria Biochemistry Laboratory, Francis Crick Institute, London NW1 1AT, UK; Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Ellen Yeh
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA; Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, USA; Division of Infectious Diseases, Columbia University Medical Center, New York, NY 10032, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
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2
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Bennett JM, Narwal SK, Kabeche S, Abegg D, Hackett F, Yeo T, Li VL, Muir RK, Faucher FF, Lovell S, Blackman MJ, Adibekian A, Yeh E, Fidock DA, Bogyo M. Mixed Alkyl/Aryl Phosphonates Identify Metabolic Serine Hydrolases as Antimalarial Targets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.11.575224. [PMID: 38260474 PMCID: PMC10802587 DOI: 10.1101/2024.01.11.575224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Malaria, caused by Plasmodium falciparum, remains a significant health burden. A barrier for developing anti-malarial drugs is the ability of the parasite to rapidly generate resistance. We demonstrated that Salinipostin A (SalA), a natural product, kills parasites by inhibiting multiple lipid metabolizing serine hydrolases, a mechanism with a low propensity for resistance. Given the difficulty of employing natural products as therapeutic agents, we synthesized a library of lipidic mixed alkyl/aryl phosphonates as bioisosteres of SalA. Two constitutional isomers exhibited divergent anti-parasitic potencies which enabled identification of therapeutically relevant targets. We also confirm that this compound kills parasites through a mechanism that is distinct from both SalA and the pan-lipase inhibitor, Orlistat. Like SalA, our compound induces only weak resistance, attributable to mutations in a single protein involved in multidrug resistance. These data suggest that mixed alkyl/aryl phosphonates are a promising, synthetically tractable anti-malarials with a low-propensity to induce resistance.
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Affiliation(s)
- John M Bennett
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Sunil K Narwal
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, USA
| | - Stephanie Kabeche
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Abegg
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | - Fiona Hackett
- Malaria Biochemistry Laboratory, Francis Crick Institute, London NW1 1AT, UK
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, USA
| | - Veronica L Li
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Ryan K Muir
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Scott Lovell
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael J Blackman
- Malaria Biochemistry Laboratory, Francis Crick Institute, London NW1 1AT, UK
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Ellen Yeh
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, USA
- Division of Infectious Diseases, Columbia University Medical Center, New York, NY 10032 USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
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3
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Yuan DQ, Tominaga T, Fukuda K, Koga K, Fukudome M. Three-in-one: Miniature Models of Natural Acyl-transfer Systems Enable Vector-selective Reaction on the Primary Side of Cyclodextrins. Chemistry 2021; 28:e202103940. [PMID: 34889479 DOI: 10.1002/chem.202103940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Indexed: 11/09/2022]
Abstract
Miniature models of acyl-transfer systems in cells, which were composed by replacing the protein, coenzyme and substrate with CD, functional group, and CD, respectively, and combining them all together in one, displayed definite role-sharing and exact cooperation of the functional groups and hydrophobic cavity, and thus enabled the regio-specific reaction.
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Affiliation(s)
- De-Qi Yuan
- Kobe Gakuin University, Faculty of Pharmaceutical Sciences, 1-1-3 Minatojima, Chuoku, 650-0056, Kobe, JAPAN
| | - Tatsuro Tominaga
- Kobe Gakuin University, Graduate School of Pharmaceutical Sciences, JAPAN
| | - Koki Fukuda
- Kobe Gakuin University, Graduate School of Pharmaceutical Sciences, JAPAN
| | - Kazutaka Koga
- Daiichi University of Pharmacy: Daiichi Yakka Daigaku, Faculty of Pharmacy, JAPAN
| | - Makoto Fukudome
- Kobe Gakuin University: Kobe Gakuin Daigaku, Faculty of Pharmaceutical Sciences, JAPAN
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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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Ji H, Shi T, Liu L, Zhang F, Tao W, Min Q, Deng Z, Bai L, Zhao Y, Zheng J. Computational studies on the substrate specificity of an acyltransferase domain from salinomycin polyketide synthase. Catal Sci Technol 2021. [DOI: 10.1039/d1cy00284h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The complex of SalAT14 and its cognate substrate EMCoA is apt to stay in a conformation suitable for the reaction. Computational investigations reveal the structural basis of AT specificity and could potentially help the engineering of modular PKSs.
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Affiliation(s)
- Huining Ji
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Liu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Fa Zhang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wentao Tao
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qing Min
- Pharmacy School, Hubei University of Science and Technology, Hubei, Xianning 437100, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yilei Zhao
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, China
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6
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Zhang F, Ji H, Ali I, Deng Z, Bai L, Zheng J. Structural and Biochemical Insight into the Recruitment of Acyl Carrier Protein-Linked Extender Units in Ansamitocin Biosynthesis. Chembiochem 2020; 21:1309-1314. [PMID: 31777147 DOI: 10.1002/cbic.201900628] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Indexed: 01/17/2023]
Abstract
A few acyltransferase (AT) domains of modular polyketide synthases (PKSs) recruit acyl carrier protein (ACP)-linked extender units with unusual C2 substituents to confer functionalities that are not available in coenzyme A (CoA)-linked ones. In this study, an AT specific for methoxymalonyl (MOM)-ACP in the third module of the ansamitocin PKS was structurally and biochemically characterized. The AT uses a conserved tryptophan residue at the entrance of the substrate binding tunnel to discriminate between different carriers. A W275R mutation switches its carrier specificity from the ACP to the CoA molecule. The acyl-AT complex structures clearly show that the MOM-ACP accepted by the AT has the 2S instead of the opposite 2R stereochemistry that is predicted according to the biosynthetic derivation from a d-glycolytic intermediate. Together, these results reveal the structural basis of ATs recognizing ACP-linked extender units in polyketide biosynthesis.
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Affiliation(s)
- Fa Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, 200240, Shanghai, P. R. China
| | - Huining Ji
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, 200240, Shanghai, P. R. China
| | - Imtiaz Ali
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, 200240, Shanghai, P. R. China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, 200240, Shanghai, P. R. China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, 200240, Shanghai, P. R. China
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, 200240, Shanghai, P. R. China
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Hayashi S, Satoh Y, Ogasawara Y, Maruyama C, Hamano Y, Ujihara T, Dairi T. Control Mechanism for cis
Double-Bond Formation by Polyunsaturated Fatty-Acid Synthases. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812623] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Shohei Hayashi
- Graduate School of Chemical Sciences and Engineering; Hokkaido University; N13-W8, Kita-ku Sapporo 060-8628 Japan
| | - Yasuharu Satoh
- Graduate School of Engineering; Hokkaido University; N13-W8, Kita-ku Sapporo 060-8628 Japan
| | - Yasushi Ogasawara
- Graduate School of Engineering; Hokkaido University; N13-W8, Kita-ku Sapporo 060-8628 Japan
| | - Chitose Maruyama
- Department of Bioscience; Fukui Prefectural University; Fukui 910-1195 Japan
| | - Yoshimitsu Hamano
- Department of Bioscience; Fukui Prefectural University; Fukui 910-1195 Japan
| | - Tetsuro Ujihara
- Kyowa Hakko Bio Co. Ltd.; 1-6-1, Ohtemachi, Chiyoda-ku Tokyo 100-8185 Japan
| | - Tohru Dairi
- Graduate School of Engineering; Hokkaido University; N13-W8, Kita-ku Sapporo 060-8628 Japan
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8
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Hayashi S, Satoh Y, Ogasawara Y, Maruyama C, Hamano Y, Ujihara T, Dairi T. Control Mechanism for cis Double-Bond Formation by Polyunsaturated Fatty-Acid Synthases. Angew Chem Int Ed Engl 2019; 58:2326-2330. [PMID: 30623559 DOI: 10.1002/anie.201812623] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 11/30/2018] [Indexed: 11/06/2022]
Abstract
Polyunsaturated fatty acids (PUFAs) such as docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), and arachidonic acid (ARA) are essential fatty acids for humans. Some microorganisms biosynthesize these PUFAs through PUFA synthases composed of four subunits with multiple catalytic domains. These PUFA synthases each create a specific PUFA without undesirable byproducts, even though the multiple catalytic domains in each large subunit are very similar. However, the detailed biosynthetic pathways and mechanisms for controlling final-product profiles are still obscure. In this study, the FabA-type dehydratase domain (DHFabA ) in the C-subunit and the polyketide synthase-type dehydratase domain (DHPKS ) in the B-subunit of ARA synthase were revealed to be essential for ARA biosynthesis by in vivo gene exchange assays. Furthermore, in vitro analysis with truncated recombinant enzymes and C4 - to C8 -acyl ACP substrates showed that ARA and EPA synthases utilized two types of DH domains, DHPKS and DHFabA , depending on the carbon-chain length, to introduce either saturation or cis double bonds to growing acyl chains.
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Affiliation(s)
- Shohei Hayashi
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, N13-W8, Kita-ku, Sapporo, 060-8628, Japan
| | - Yasuharu Satoh
- Graduate School of Engineering, Hokkaido University, N13-W8, Kita-ku, Sapporo, 060-8628, Japan
| | - Yasushi Ogasawara
- Graduate School of Engineering, Hokkaido University, N13-W8, Kita-ku, Sapporo, 060-8628, Japan
| | - Chitose Maruyama
- Department of Bioscience, Fukui Prefectural University, Fukui, 910-1195, Japan
| | - Yoshimitsu Hamano
- Department of Bioscience, Fukui Prefectural University, Fukui, 910-1195, Japan
| | - Tetsuro Ujihara
- Kyowa Hakko Bio Co. Ltd., 1-6-1, Ohtemachi, Chiyoda-ku, Tokyo, 100-8185, Japan
| | - Tohru Dairi
- Graduate School of Engineering, Hokkaido University, N13-W8, Kita-ku, Sapporo, 060-8628, Japan
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Santín O, Moncalián G. Loading of malonyl-CoA onto tandem acyl carrier protein domains of polyunsaturated fatty acid synthases. J Biol Chem 2018; 293:12491-12501. [PMID: 29921583 DOI: 10.1074/jbc.ra118.002443] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 06/04/2018] [Indexed: 12/13/2022] Open
Abstract
Omega-3 polyunsaturated fatty acids (PUFA) are produced in some unicellular organisms, such as marine gammaproteobacteria, myxobacteria, and thraustochytrids, by large enzyme complexes called PUFA synthases. These enzymatic complexes resemble bacterial antibiotic-producing proteins known as polyketide synthases (PKS). One of the PUFA synthase subunits is a conserved large protein (PfaA in marine proteobacteria) that contains three to nine tandem acyl carrier protein (ACP) domains as well as condensation and modification domains. In this work, a study of the PfaA architecture and its ability to initiate the synthesis by selecting malonyl units has been carried out. As a result, we have observed a self-acylation ability in tandem ACPs whose biochemical mechanism differ from the previously described for type II PKS. The acyltransferase domain of PfaA showed a high selectivity for malonyl-CoA that efficiently loads onto the ACPs domains. These results, together with the structural organization predicted for PfaA, suggest that this protein plays a key role at early stages of the anaerobic pathway of PUFA synthesis.
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Affiliation(s)
- Omar Santín
- From the Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria, 39011 Santander, Spain
| | - Gabriel Moncalián
- From the Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria, 39011 Santander, Spain
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Liu Y, Feng Y, Wang Y, Li X, Cao X, Xue S. Structural and biochemical characterization of MCAT from photosynthetic microorganism Synechocystis sp. PCC 6803 reveal its stepwise catalytic mechanism. Biochem Biophys Res Commun 2015; 457:398-403. [DOI: 10.1016/j.bbrc.2015.01.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Accepted: 01/03/2015] [Indexed: 11/26/2022]
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