title: DOM-fold: a structure with crossing loops found in DmpA, ornithine acetyltransferase, and molybdenum cofactor-binding domain.
abstract: Understanding relationships between sequence, structure, and evolution is important for functional characterization of proteins. Here, we define a novel DOM-fold as a consensus structure of the domains in DmpA (L-aminopeptidase D-Ala-esterase/amidase), OAT (ornithine acetyltransferase), and MocoBD (molybdenum cofactor-binding domain), and discuss possible evolutionary scenarios of its origin. As shown by a comprehensive structure similarity search, DOM-fold distinguished by a two-layered beta/alpha architecture of a particular topology with unusual crossing loops is unique to those three protein families. DmpA and OAT are evolutionarily related as indicated by their sequence, structural, and functional similarities. Structural similarity between the DmpA/OAT superfamily and the MocoBD domains has not been reported before. Contrary to previous reports, we conclude that functional similarities between DmpA/OAT proteins and N-terminal nucleophile (Ntn) hydrolases are convergent and are unlikely to be inherited from a common ancestor.
authors.affiliation: Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, 75390-9050, USA.
authors.forename: Hua
authors.initials: H
authors.lastname: Cheng
authors.forename: Nick V
authors.initials: NV
authors.lastname: Grishin
mesh_terms: D000123:Acetyltransferases / Q000737:chemistry*; D000581:Amidohydrolases / Q000737:chemistry*; D000595:Amino Acid Sequence; D000626:Aminopeptidases / Q000737:chemistry*; D001426:Bacterial Proteins / Q000737:chemistry*; D001665:Binding Sites; D003067:Coenzymes / Q000737:chemistry / Q000378:metabolism*; D019143:Evolution, Molecular; D008667:Metalloproteins / Q000737:chemistry / Q000378:metabolism*; D008969:Molecular Sequence Data; D000090006:Molybdenum Cofactors; D020621:Ochrobactrum anthropi / Q000201:enzymology; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011621:Pteridines / Q000737:chemistry / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid
chemical_list: D000123:Acetyltransferases; D000581:Amidohydrolases; D000626:Aminopeptidases; D001426:Bacterial Proteins; D003067:Coenzymes; D008667:Metalloproteins; D000090006:Molybdenum Cofactors; D011621:Pteridines; C022261:molybdopterin; C020646:glutamate acetyltransferase; C118321:DmpA protein, Ochrobactrum anthropi; C438834:N-terminal nucleophile hydrolase