Protein Family Models

A winged helix-turn-helix domain present in the plant HB1, vertebrate ASXL, the H. pylori restriction endonuclease HpyAIII(HgrA), the RNA polymerase delta subunit(RpoE) of Gram positive bacteria and several restriction endonucleases [1]. The domain is distinguished by the presence of a conserved one-turn helix between helix-3 and the preceding conserved turn. Its diverse architectures in eukaryotic species with extensive gene body methylation is suggestive of a chromatin function. The genetic interaction of the HARE-HTH containing ASXL with the methyl cytosine hydroxylating Tet2 protein is suggestive of a role for the domain in discriminating sequences with DNA modifications such as hmC [1]. Bacterial versions include fusions to diverse restriction endonucleases, and a DNA glycosylase where it may play a similar role in detecting modified DNA. Certain bacterial version of the HARE-HTH domain show fusions to the helix-hairpin-helix domain of the RNA polymerase alpha subunit and the HTH domains found in regions 3 and 4 of the sigma factors [1]. These versions are predicted to function as a novel inhibitor of the binding of RNA polymerase to transcription start sites, similar to the Bacillus delta protein [2,3]. [1]. 10336502. Expression, abundance, and RNA polymerase binding properties of the delta factor of Bacillus subtilis. Lopez de Saro FJ, Yoshikawa N, Helmann JD;. J Biol Chem 1999;274:15953-15958. [2]. 7545758. Structural analysis of the Bacillus subtilis delta factor: a protein polyanion which displaces RNA from RNA polymerase. Lopez de Saro FJ, Woody AY, Helmann JD;. J Mol Biol 1995;252:189-202. [3]. 22186017. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-10-16

Members of this family are the RNA polymerase delta subunit, as found in the Firmicutes and the Mollicutes. All members of the seed alignment have an extended C-terminal low-complexity region, consisting largely of Asp and Glu, that is not included in the model. Proteins giving borderline scores should be checked to confirm a similar acidic C-terminal domain.

Gene:

rpoE

Date:

2024-05-29

DNA-directed RNA polymerase subunit delta participates in both the initiation and recycling phases of transcription

Date:

2024-11-05