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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.

June 2008 / First entry.

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

CID, PS51391; CID domain profile  (MATRIX)

Sequences known to belong to this class detected by the profile: ALL Other sequence(s) detected in Swiss-Prot: NONE

• Domain architecture view of Swiss-Prot proteins matching PS51391 • 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 PS51391 • Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS51391 • Scan Swiss-Prot/TrEMBL entries against PS51391 • view ligand binding statistics

Matching PDB structures: 1SZ9 1SZA 2BF0 2DIW ... [ALL]

1	Authors	Meinhart A., Cramer P.
	Title	Recognition of RNA polymerase II carboxy-terminal domain by 3'-RNA-processing factors.
	Source	Nature 430:223-226(2004).
	PubMed ID	15241417
	DOI	10.1038/nature02679

2	Authors	Noble C.G., Hollingworth D., Martin S.R., Ennis-Adeniran V., Smerdon S.J., Kelly G., Taylor I.A., Ramos A.
	Title	Key features of the interaction between Pcf11 CID and RNA polymerase II CTD.
	Source	Nat. Struct. Mol. Biol. 12:144-151(2005).
	PubMed ID	15665873
	DOI	10.1038/nsmb887

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