InterPro domain: IPR002078

Some bacterial regulatory proteins activate the expression of genes frompromoters recognised by core RNA polymerase associated with the alternativesigma-54 factor. These have a conserved domain of about 230 residues involvedin the ATP-dependent [ 1 , 2 ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [ 3 ] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section.

The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction [ 4 ]. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.

1. The sigma 54 bacterial enhancer-binding protein family: mechanism of action and phylogenetic relationship of their functional domains. J. Bacteriol. 175, 6067-74
2. Influence of a mutation in the putative nucleotide binding site of the nitrogen regulatory protein NTRC on its positive control function. Nucleic Acids Res. 19, 2281-7
3. Prokaryotic signal transduction mediated by sensor and regulator protein pairs. Annu. Rev. Genet. 23, 311-36
4. The prokaryotic enhancer binding protein NTRC has an ATPase activity which is phosphorylation and DNA dependent. EMBO J. 11, 2219-28