PROSITE documentation PDOC51391
CID domain profile


The C-terminal domain (CTD) of the large subunit of RNA polymerase II is a platform for mRNA processing factors and links gene transcription to mRNA capping, splicing and polyadenylation. CTD recognition is dependent on the phosphorylation state of the CTD itself, which varies during the course of transcription but has also been linked to the isomerization state of the CTD's proline residues. Several RNA-processing factors recognize the CTD by means of a conserved CTD-interacting domain (CID). Factors with CID domains include the serine/arginine-rich-like factors SCAF4 and SCAF8, Nrd1 (which is implicated in polyadenylation-independent RNA 3'-end formation) and Pcf11. Pcf11 is a conserved and essential subunit of the yeast cleavage factor 1A, which is required for 3'-RNA processing and transcription termination [1,2].

The CID domain is a right-handed superhelix of eight α-helices forming a compact domain (see <PDB:1SZ9>). The CID fold closely resembles that of VHS domains (see <PDOC50179>) and is related to armadillo-repeat proteins (see (<PDOC50176>), except for the two amino-terminal helices. Amino acid residues in the hydrophobic core of the domain are highly conserved across CID domains [1,2].

The profile we developed covers the entire CID domain.

Last update:

June 2008 / First entry.


Technical section

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

CID, PS51391; CID domain profile  (MATRIX)


1AuthorsMeinhart A. Cramer P.
TitleRecognition of RNA polymerase II carboxy-terminal domain by 3'-RNA-processing factors.
SourceNature 430:223-226(2004).
PubMed ID15241417

2AuthorsNoble C.G. Hollingworth D. Martin S.R. Ennis-Adeniran V. Smerdon S.J. Kelly G. Taylor I.A. Ramos A.
TitleKey features of the interaction between Pcf11 CID and RNA polymerase II CTD.
SourceNat. Struct. Mol. Biol. 12:144-151(2005).
PubMed ID15665873

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