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FOR THE RECORD

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

¹ Department of Biochemistry and ² Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050, USA

(RECEIVED January 16, 2005; FINAL REVISION April 1, 2005; ACCEPTED April 8, 2005)

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 / 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.

Keywords: DmpA; NylC; OAT; Ntn hydrolases; molybdenum cofactor-binding domain; convergent evolution; divergent evolution; duplication and fusion; domain swapping

Abbreviations: PDB, Protein Data Bank • DmpA, L-aminopeptidase D-Ala-esterase/amidase • OAT, ornithine acetyltransferase • MocoBD, molybdenum cofactor-binding domain • Ntn, N-terminal nucleophile • PSI-BLAST, Position-Specific Iterated Basic Local Alignment Search Tool • RMSD, root mean square deviation

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.051364905.

Reprint requests to: Nick V. Grishin, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9050, USA; e-mail: grishin{at}chop.swmed.edu; fax: (214) 648-9099.

Supplemental material: see www.proteinscience.org

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