DOM-fold: A structure with crossing loops found in DmpA, ornithine acetyltransferase, and molybdenum cofactor-binding domain

Hua Cheng, Nick V. Grishin

Research output: Contribution to journalArticle

24 Scopus citations

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 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.

Original languageEnglish (US)
Pages (from-to)1902-1910
Number of pages9
JournalProtein Science
Volume14
Issue number7
DOIs
StatePublished - Jul 2005

Keywords

  • Convergent evolution
  • Divergent evolution
  • DmpA
  • Domain swapping
  • Duplication and fusion
  • Molybdenum cofactor-binding domain
  • Ntn hydrolases
  • NylC
  • OAT

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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