title: Structure and functional characterization of a bile acid 7α dehydratase BaiE in secondary bile acid synthesis.
abstract: Conversion of the primary bile acids cholic acid (CA) and chenodeoxycholic acid (CDCA) to the secondary bile acids deoxycholic acid (DCA) and lithocholic acid (LCA) is performed by a few species of intestinal bacteria in the genus Clostridium through a multistep biochemical pathway that removes a 7α-hydroxyl group. The rate-determining enzyme in this pathway is bile acid 7α-dehydratase (baiE). In this study, crystal structures of apo-BaiE and its putative product-bound [3-oxo-Δ(4,6) -lithocholyl-Coenzyme A (CoA)] complex are reported. BaiE is a trimer with a twisted α + β barrel fold with similarity to the Nuclear Transport Factor 2 (NTF2) superfamily. Tyr30, Asp35, and His83 form a catalytic triad that is conserved across this family. Site-directed mutagenesis of BaiE from Clostridium scindens VPI 12708 confirm that these residues are essential for catalysis and also the importance of other conserved residues, Tyr54 and Arg146, which are involved in substrate binding and affect catalytic turnover. Steady-state kinetic studies reveal that the BaiE homologs are able to turn over 3-oxo-Δ(4) -bile acid and CoA-conjugated 3-oxo-Δ(4) -bile acid substrates with comparable efficiency questioning the role of CoA-conjugation in the bile acid metabolism pathway.
authors.affiliation: Joint Center for Structural Genomics, (http://www.jcsg.org).|Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037.
authors.forename: Shiva
authors.initials: S
authors.lastname: Bhowmik
authors.affiliation: Genomics Institute of Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California, 92121.
authors.forename: Hsien-Po
authors.initials: HP
authors.lastname: Chiu
authors.affiliation: Genomics Institute of Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California, 92121.
authors.forename: David H
authors.initials: DH
authors.lastname: Jones
authors.affiliation: Joint Center for Structural Genomics, (http://www.jcsg.org).|Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, MS 9, Menlo Park, California, 94025.
authors.forename: Hsiu-Ju
authors.initials: HJ
authors.lastname: Chiu
authors.affiliation: Joint Center for Structural Genomics, (http://www.jcsg.org).|Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, MS 9, Menlo Park, California, 94025.
authors.forename: Mitchell D
authors.initials: MD
authors.lastname: Miller
authors.affiliation: Joint Center for Structural Genomics, (http://www.jcsg.org).|Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, MS 9, Menlo Park, California, 94025.
authors.forename: Qingping
authors.initials: Q
authors.lastname: Xu
authors.affiliation: Joint Center for Structural Genomics, (http://www.jcsg.org).|Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037.
authors.forename: Carol L
authors.initials: CL
authors.lastname: Farr
authors.affiliation: Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, 23298.|McGuire VA Medical Center, Richmond, Virginia, 23298.
authors.forename: Jason M
authors.initials: JM
authors.lastname: Ridlon
authors.affiliation: USDA ARS, US Meat Animal Research Center, Clay Center, Nebraska, 68933.
authors.forename: James E
authors.initials: JE
authors.lastname: Wells
authors.affiliation: Joint Center for Structural Genomics, (http://www.jcsg.org).|Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037.
authors.forename: Marc-André
authors.initials: MA
authors.lastname: Elsliger
authors.affiliation: Joint Center for Structural Genomics, (http://www.jcsg.org).|Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037.
authors.forename: Ian A
authors.initials: IA
authors.lastname: Wilson
authors.affiliation: Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, 23298.|McGuire VA Medical Center, Richmond, Virginia, 23298.
authors.forename: Phillip B
authors.initials: PB
authors.lastname: Hylemon
authors.affiliation: Joint Center for Structural Genomics, (http://www.jcsg.org).|Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037.|Genomics Institute of Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California, 92121.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Lesley
mesh_terms: D019943:Amino Acid Substitution; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics; D020134:Catalytic Domain; D002793:Cholic Acids / Q000096:biosynthesis / Q000737:chemistry*; D003013:Clostridium / Q000201:enzymology*; D018360:Crystallography, X-Ray; D006801:Humans; D006836:Hydro-Lyases / Q000737:chemistry* / Q000235:genetics; D006860:Hydrogen Bonding; D006900:Hydroxylation; D007700:Kinetics; D062105:Molecular Docking Simulation; D016297:Mutagenesis, Site-Directed; D011485:Protein Binding; D017433:Protein Structure, Secondary; D040681:Structural Homology, Protein
chemical_list: D001426:Bacterial Proteins; D002793:Cholic Acids; D006836:Hydro-Lyases; C102989:baiE protein, Clostridium scindens
keywords: 7α-dehyroxylation; bile acid 7α-dehydratase; gut microbe mediated human metabolite; gut microbes; nuclear transport factor-2 superfamily; primary bile acid; secondary bile acid; secondary bile acid synthesis; structural genomics