Six Rossmannoid folds, including the Class I aminoacyl-tRNA synthetases, share a partial core with the anti-codon-binding domain of a Class II aminoacyl-tRNA synthetase.

ABSTRACT:

Motivation

Similarities in core residue packing provide evidence for divergence or convergence not reported using other methods.

Results

We apply a new method for rapid structure comparison based on Simplicial Neighborhood Analysis of Protein Packing (SNAPP) to the diverse structural classification of proteins (SCOP) alpha/beta-class of protein folds. The procedure identifies inter-residue packing motifs shared by protein pairs from different folds. A threshold of 0.67 A RMSD for all atoms of corresponding residues ensures inclusion of only highly significant similarities comparable with those observed for identical catalytic residues in homologues. Many tertiary packing motifs are shared among the three classical Rossmannoid folds, as well as thousands of other motifs that

SUBMITTER: Cammer S 

PROVIDER: S-EPMC2852213 | biostudies-literature | 2010 Mar

REPOSITORIES: biostudies-literature