Domains genome-wide analysis

Genome-Wide Analysis New Quality in Domain Research. 89... 

The putative kinase domains are not highly conserved over evolution. The N-terminal kinase domain has weak similarity to a protein kinase family, whereas the C-terminal domains shows no similarity to any known kinase. Further characterization of the N-terminal kinase domain indicates that acidic residues in two small regions are important for the kinase activity (O Brien and Tjian, 1998). Combined mutation of both regions disrupts kinase activity, and the mutant has reduced ability to rescue the ts 13 cell line, a ts hamster cell line with a mutation in TAFl. This mutant shows a defect in transcription of approximately 6% in a genome-wide analysis (O Brien and Tjian, 2000), indicating that the kinase activity of the N-terminal domain may be required for expression of a subset of genes in vivo. 

An analysis of 40 genomes representing all three kingdoms of life identified 1307 pairwise combinations of 783 domains. Only a small proportion of domains (1%) has been used extensively in combinations with other domains. In multidomain enzymes, the P-loop nucleotide triphosphate hydrolase domain and the Rossman fold (which binds NAD /NADH) are the most commonly found. The P-loop hydrolase domain is associated with 47 and 21 different domain partners in bacteria and Archaea, respectively, and the Rossman fold with 29 and 18 domain partners in bacteria and Archaea, respectively. The repeated use of these domains reflects the utility of the reactions they facilitate - phosphoryl transfer and hydride transfer. By combining these domains with a domain that provides substrate specificity, a wide range of reactions can be accomplished without a need to reinvent something that already works well. 

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