title: Structural Basis for Substrate Specificity in Adenosylcobalamin-dependent Isobutyryl-CoA Mutase and Related Acyl-CoA Mutases.
abstract: Acyl-CoA mutases are a growing class of adenosylcobalamin-dependent radical enzymes that perform challenging carbon skeleton rearrangements in primary and secondary metabolism. Members of this class of enzymes must precisely control substrate positioning to prevent oxidative interception of radical intermediates during catalysis. Our understanding of substrate specificity and catalysis in acyl-CoA mutases, however, is incomplete. Here, we present crystal structures of IcmF, a natural fusion protein variant of isobutyryl-CoA mutase, in complex with the adenosylcobalamin cofactor and four different acyl-CoA substrates. These structures demonstrate how the active site is designed to accommodate the aliphatic acyl chains of each substrate. The structures suggest that a conformational change of the 5'-deoxyadenosyl group from C2'-endo to C3'-endo could contribute to initiation of catalysis. Furthermore, detailed bioinformatic analyses guided by our structural findings identify critical determinants of acyl-CoA mutase substrate specificity and predict new acyl-CoA mutase-catalyzed reactions. These results expand our understanding of the substrate specificity and the catalytic scope of acyl-CoA mutases and could benefit engineering efforts for biotechnological applications ranging from production of biofuels and commercial products to hydrocarbon remediation.
authors: Departments of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139.
authors: Marco
authors: M
authors: Jost
authors: Departments of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; the Graduate Program in Biophysics, Harvard University, Cambridge, Massachusetts 02138.
authors: David A
authors: DA
authors: Born
authors: Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-0600.
authors: Valentin
authors: V
authors: Cracan
authors: Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-0600.
authors: Ruma
authors: R
authors: Banerjee
authors: Departments of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; Departments of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139,. Electronic address: cdrennan@mit.edu.
authors: Catherine L
authors: CL
authors: Drennan
mesh_terms: D000214:Acyl Coenzyme A / Q000378:metabolism; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D020134:Catalytic Domain / Q000235:genetics; D003038:Cobamides / Q000378:metabolism; D018360:Crystallography, X-Ray; D049921:Cupriavidus / Q000201:enzymology / Q000235:genetics; D019751:Intramolecular Transferases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D011487:Protein Conformation; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D017386:Sequence Homology, Amino Acid; D040681:Structural Homology, Protein; D013379:Substrate Specificity
chemical_list: D000214:Acyl Coenzyme A; D001426:Bacterial Proteins; D003038:Cobamides; D011994:Recombinant Proteins; C050106:isobutyryl-coenzyme A; D019751:Intramolecular Transferases; C000913:cobamamide
keywords: acyl-CoA mutase; adenosylcobalamin (AdoCbl); enzyme catalysis; metalloenzyme; substrate specificity; x-ray crystallography