Using shifts in amino acid frequency and substitution rate to identify latent structural characters in base-excision repair enzymes.

ABSTRACT: Protein evolution includes the birth and death of structural motifs. For example, a zinc finger or a salt bridge may be present in some, but not all, members of a protein family. We propose that such transitions are manifest in sequence phylogenies as concerted shifts in substitution rates of amino acids that are neighbors in a representative structure. First, we identified rate shifts in a quartet from the Fpg/Nei family of base excision repair enzymes using a method developed by Xun Gu and coworkers. We found the shifts to be spatially correlated, more precisely, associated with a flexible loop involved in bacterial Fpg substrate specificity. Consistent with our result, sequences and structures provide convincing evidence that this loop plays a very different role in other family members

SUBMITTER: Barrantes-Reynolds R 

PROVIDER: S-EPMC3188539 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature