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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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Chan S, Giuroiu I, Chernishof I, Sawaya MR, Chiang J, Gunsalus RP, Arbing MA, Perry LJ. Apo and ligand-bound structures of ModA from the archaeon Methanosarcina acetivorans. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:242-50. [PMID: 20208152 PMCID: PMC2833028 DOI: 10.1107/s1744309109055158] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Accepted: 12/22/2009] [Indexed: 11/10/2022]
Abstract
The trace-element oxyanion molybdate, which is required for the growth of many bacterial and archaeal species, is transported into the cell by an ATP-binding cassette (ABC) transporter superfamily uptake system called ModABC. ModABC consists of the ModA periplasmic solute-binding protein, the integral membrane-transport protein ModB and the ATP-binding and hydrolysis cassette protein ModC. In this study, X-ray crystal structures of ModA from the archaeon Methanosarcina acetivorans (MaModA) have been determined in the apoprotein conformation at 1.95 and 1.69 A resolution and in the molybdate-bound conformation at 2.25 and 2.45 A resolution. The overall domain structure of MaModA is similar to other ModA proteins in that it has a bilobal structure in which two mixed alpha/beta domains are linked by a hinge region. The apo MaModA is the first unliganded archaeal ModA structure to be determined: it exhibits a deep cleft between the two domains and confirms that upon binding ligand one domain is rotated towards the other by a hinge-bending motion, which is consistent with the 'Venus flytrap' model seen for bacterial-type periplasmic binding proteins. In contrast to the bacterial ModA structures, which have tetrahedral coordination of their metal substrates, molybdate-bound MaModA employs octahedral coordination of its substrate like other archaeal ModA proteins.
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Affiliation(s)
- Sum Chan
- UCLA–DOE Institute for Genomics and Proteomics, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Iulia Giuroiu
- UCLA–DOE Institute for Genomics and Proteomics, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Irina Chernishof
- UCLA–DOE Institute for Genomics and Proteomics, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Michael R. Sawaya
- UCLA–DOE Institute for Genomics and Proteomics, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Janet Chiang
- UCLA–DOE Institute for Genomics and Proteomics, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Robert P. Gunsalus
- UCLA–DOE Institute for Genomics and Proteomics, University of California at Los Angeles, Los Angeles, CA 90095, USA
- The Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Mark A. Arbing
- UCLA–DOE Institute for Genomics and Proteomics, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - L. Jeanne Perry
- UCLA–DOE Institute for Genomics and Proteomics, University of California at Los Angeles, Los Angeles, CA 90095, USA
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