rapA group

The rapA group includes some 220 members and shows significantly more sequence variation than other subfamilies. Subsets of sequences are qualitatively visible within multiple alignments of the group, but initial attempts to distinguish them have been unreliable due to the variability of microbial sequences and non-homogeneous sampling in sequenced organisms (eg half of all complete bacterial genomes are for a limited range of firmicute and gamma proteobacterial genera).

Although the rapA group contains the conserved sequence patterns of the Snf2 family for the classical helicase-like motifs, other conserved blocks cannot be easily identified. The characteristic extended span of at least 160 residues between helicase motifs III and IV 3 is maintained in the rapA group, but the central part of this region diverges markedly from the other subfamilies and lacks the highly conserved features characteristic of the Snf2 family. The specific difficulty of aligning this region has previously been remarked upon 4.

The archetype and only member of this group for which biological function has been investigated is E coli rapA, also known as HepA 1. This enzyme influences polymerase recycling under high salt conditions, possibly by aiding the release of stalled polymerases 2.

The rapA group also includes a number of polypeptides for which the helicase-like region comprises effectively the entire polypeptide. This is unlike other Snf2 family members which almost universally contain domains or domain-sized sequences outside the helicase-like region which are likely to form accessory domains or interaction surfaces.

names associated with members
1: Muzzin, O., E. A. Campbell, et al. (1998). Disruption of Escherichia coli hepA, an RNA polymerase-associated protein, causes UV sensitivity. J Biol Chem 273(24): 15157-61. PubMed
2: Sukhodolets, M. V., J. E. Cabrera, et al. (2001). RapA, a bacterial homolog of SWI2/SNF2, stimulates RNA polymerase recycling in transcription. Genes Dev 15(24): 3330-41. PubMed
3: Flaus, A. and T. Owen-Hughes (2001). Mechanisms for ATP-dependent chromatin remodelling. Curr Opin Genet Dev 11(2): 148-54. PubMed
4: Eisen, J. A., K. S. Sweder, et al. (1995). Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic Acids Res 23(14): 2715-23. PubMed