Taxonomic distribution of proteins containing VRR_NUC domains

The tree below includes only several representative species and genera. The complete taxonomic breakdown of all proteins containing VRR_NUC domains can be accessed here. Click the counts or percentage values to display the corresponding proteins.

Identification of novel restriction endonuclease-like fold families amonghypothetical proteins.

Kinch LN, Ginalski K, Rychlewski L, Grishin NV
Nucleic Acids Res. 2005; 33: 3598-605

Restriction endonucleases and other nucleic acid cleaving enzymes form alarge and extremely diverse superfamily that display little sequencesimilarity despite retaining a common core fold responsible for cleavage.The lack of significant sequence similarity between protein families makeshomology inference a challenging task and hinders new familyidentification with traditional sequence-based approaches. Using theconsensus fold recognition method Meta-BASIC that combines sequenceprofiles with predicted protein secondary structure, we identify nine newrestriction endonuclease-like fold families among previouslyuncharacterized proteins and predict these proteins to cleave nucleic acidsubstrates. Application of transitive searches combined with geneneighborhood analysis allow us to confidently link these unknown familiesto a number of known restriction endonuclease-like structures and thusassign folds to the uncharacterized proteins. Finally, our methodidentifies a novel restriction endonuclease-like domain in the C-terminusof RecC that is not detected with structure-based searches of the existingPDB database.