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PDOC00854

RNA polymerases H / 23 Kd subunits signature

Description:

In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (EC 2.7.7.6) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides.

Archaebacterial subunit H (gene rpoH) [1,2] is a small protein of about 8.5 to 10 Kd, it is evolutionary related to the C-terminal part of a 23 Kd component shared by all three forms of eukaryotic RNA polymerases (gene RPB5 in yeast and POLR2E in mammals).

As a signature pattern we selected a conserved region which is located at the N-terminal extremity of subunit H; this region contains two histidines that could play a role in the binding of a metal ion.

Last update:

December 2004 / Pattern and text revised.

Technical section:

PROSITE method (with tools and information) covered by this documentation:

RNA_POL_H_23KD, PS01110; RNA polymerases H / 23 Kd subunits signature  (PATTERN)
Consensus pattern: H - [NQEIVMYD] - [LIVMYAS] - V - P - [EKT] - H - x(2) - [LIVM] - x(2) - [DESAG] - [ET]
Sequences known to belong to this class detected by the pattern: ALL
Other sequence(s) detected in Swiss-Prot: NONE
• Retrieve an alignment of Swiss-Prot true positive hits:
  Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format
• Retrieve the sequence logo from the alignment
• Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS01110
• Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS01110
• Scan Swiss-Prot/TrEMBL entries against PS01110
• view ligand binding statistics
Matching PDB structures: 1DZF 1EIK 1I3Q 1I50 ... [ALL]

References:

1 AuthorsKlenk H.-P., Palm P., Lottspeich F., Zillig W.
TitleComponent H of the DNA-dependent RNA polymerases of Archaea is homologous to a subunit shared by the three eucaryal nuclear RNA polymerases.
SourceProc. Natl. Acad. Sci. U.S.A. 89:407-410(1992).
PubMed ID1729711
2 AuthorsThiru A., Hodach M., Eloranta J.J., Kostourou V., Weinzierl R.O., Matthews S.
TitleRNA polymerase subunit H features a beta-ribbon motif within a novel fold that is present in archaea and eukaryotes.
SourceJ. Mol. Biol. 287:753-760(1999).
PubMed ID10191143

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