InterPro domain: IPR006569

The C-terminal domain (CTD) of the large subunit of RNA polymerase II is aplatform for mRNA processing factors and links gene transcription to mRNAcapping, splicing and polyadenylation. CTD recognition is dependent on thephosphorylation state of the CTD itself, which varies during the course oftranscription but has also been linked to the isomerization state of the CTD'sproline residues. Several RNA-processing factors recognise the CTD by means ofa conserved CTD-interacting domain (CID). Factors with CID domains include theserine/arginine-rich-like factors SCAF4 and SCAF8, Nrd1 (which is implicatedin polyadenylation-independent RNA 3'-end formation) and Pcf11. Pcf11 is aconserved and essential subunit of the yeast cleavage factor 1A, which isrequired for 3'-RNA processing and transcription termination [ 1 , 2 ].

The CID domain is a right-handed superhelix of eight alpha-helices forming acompact domain. The CID fold closely resembles that of VHSdomains IPR002014 and is related to armadillo-repeat proteins IPR000225 , except for the two amino-terminal helices. Amino acid residuesin the hydrophobic core of the domain are highly conserved across CID domains[ 3 , 3 ].

1. Recognition of RNA polymerase II carboxy-terminal domain by 3'-RNA-processing factors. Nature 430, 223-6
2. Key features of the interaction between Pcf11 CID and RNA polymerase II CTD. Nat. Struct. Mol. Biol. 12, 144-51