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DOM‐fold: A structure with crossing loops found in DmpA, ornithine acetyltransferase, and molybdenum cofactor‐binding domain
Author(s) -
Cheng Hua,
Grishin Nick V.
Publication year - 2005
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.051364905
Subject(s) - cofactor , fold (higher order function) , molybdenum cofactor , molybdenum , chemistry , biochemistry , biology , enzyme , computer science , inorganic chemistry , programming language
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 D mpA (L‐aminopeptidase D‐Ala‐esterase/amidase), O AT (ornithine acetyltransferase), and M ocoBD (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 β/α 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.