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PROSITE documentation PDOC00411

RNA polymerases D / 30 to 40 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.

It has been shown [1,2,3] that small subunits of about 30 to 40 Kd found in all three types of eukaryotic polymerases are highly conserved. Subunits known to belong to this family are:

  • Budding yeast RPC5 subunit (or RPC40) from RNA polymerases I and III.
  • Mammalian RPA40 from RNA polymerase I.
  • Budding yeast RPB3 subunit from RNA polymerase II.
  • Fission yeast rpb3 subunit from RNA polymerase II.
  • Mammalian RPB3 (or RPB33) (gene POLR2C) from RNA polymerase II.
  • Conjugation stage-specific protein cnjC from Tetrahymena thermophila, which may be a stage-specific RNA polymerase subunit.
  • Archebacterial RNA polymerase subunit D (gene rpoD).

As a signature pattern for these subunits, we selected a conserved region in their N-terminal part.

Last update:

December 2004 / Pattern and text revised.

Technical section:

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

RNA_POL_D_30KD, PS00446; RNA polymerases D / 30 to 40 Kd subunits signature  (PATTERN)
Consensus pattern: N-[SGAT]-[LIVMF]-R-R-x(9)-[SAR]-x(3)-[VA]-x(4)-N-x-[STA]-x(3)-[DN]-E-x-[LIV]-[GSA]-x-R-[LI]-[GAS]-[LIVM](2)-[PV]
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 PS00446
• Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS00446
• Scan Swiss-Prot/TrEMBL entries against PS00446
• view ligand binding statistics
Matching PDB structures: 1I3Q 1I50 1I6H 1K83 ... [ALL]

References:

1 AuthorsKolodziej P., Young R.A.
TitleRNA polymerase II subunit RPB3 is an essential component of the mRNA transcription apparatus.
SourceMol. Cell. Biol. 9:5387-5394(1989).
PubMed ID2685562
2 AuthorsPati U.K., Weissman S.M.
TitleThe amino acid sequence of the human RNA polymerase II 33-kDa subunit hRPB 33 is highly conserved among eukaryotes.
SourceJ. Biol. Chem. 265:8400-8403(1990).
PubMed ID2187864
3 AuthorsAzuma Y., Yamagishi M., Ishihama A.
TitleSubunits of the Schizosaccharomyces pombe RNA polymerase II: enzyme purification and structure of the subunit 3 gene.
SourceNucleic Acids Res. 21:3749-3754(1993).
PubMed ID8367291

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