Taxonomic distribution of proteins containing V4R domains

The tree below includes only several representative species and genera. The complete taxonomic breakdown of all proteins containing V4R domains can be accessed here. Click the counts or percentage values to display the corresponding proteins.

Regulatory potential, phyletic distribution and evolution of ancient,intracellular small-molecule-binding domains.

Anantharaman V, Koonin EV, Aravind L
J Mol Biol. 2001; 307: 1271-92

Central cellular functions such as metabolism, solute transport and signaltransduction are regulated, in part, via binding of small molecules byspecialized domains. Using sensitive methods for sequence profile analysisand protein structure comparison, we exhaustively surveyed the proteinsets from completely sequenced genomes for all occurrences of 21intracellular small-molecule-binding domains (SMBDs) that are representedin at least two of the three major divisions of life (bacteria, archaeaand eukaryotes). These included previously characterized domains such asPAS, GAF, ACT and ferredoxins, as well as three newly predicted SMBDs,namely the 4-vinyl reductase (4VR) domain, the NIFX domain and the3-histidines (3H) domain. Although there are only a limited number ofdifferent superfamilies of these ancient SMBDs, they are present innumerous distinct proteins combined with various enzymatic, transport andsignal-transducing domains. Most of the SMBDs show considerableevolutionary mobility and are involved in the generation of manylineage-specific domain architectures. Frequent re-invention of analogousarchitectures involving functionally related, but not homologous, domainswas detected, such as, fusion of different SMBDs to several types ofDNA-binding domains to form diverse transcription regulators inprokaryotes and eukaryotes. This is suggestive of similar selective forcesaffecting the diverse SMBDs and resulting in the formation of multidomainproteins that fit a limited number of functional stereotypes. Using the"guilt by association approach", the identification of SMBDs allowedprediction of functions and mode of regulation for a variety of previouslyuncharacterized proteins.