Distribution and prediction of catalytic domains in 2-oxoglutarate dependent dioxygenases.

ABSTRACT:

Background

The 2-oxoglutarate dependent superfamily is a diverse group of non-haem dioxygenases, and is present in prokaryotes, eukaryotes, and archaea. The enzymes differ in substrate preference and reaction chemistry, a factor that precludes their classification by homology studies and electronic annotation schemes alone. In this work, I propose and explore the rationale of using substrates to classify structurally similar alpha-ketoglutarate dependent enzymes.

Findings

Differential catalysis in phylogenetic clades of 2-OG dependent enzymes, is determined by the interactions of a subset of active-site amino acids. Identifying these with existing computational methods is challenging and not feasible for all proteins. A clustering protocol based on validated mechanisms of ca

SUBMITTER: Kundu S 

PROVIDER: S-EPMC3475032 | biostudies-literature | 2012 Aug

REPOSITORIES: biostudies-literature