CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing proteins
This family is composed of Regulation of nuclear pre-mRNA domain-containing proteins 1A (RPRD1A), 1B (RPRD1B), 2 (RPRD2), yeast Rtt103, and similar proteins. RPRD1A, RPRD1B, and RPRD2 are CID (CTD-Interacting Domain) containing proteins that co-purify with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. Yeast transcription termination factor Rtt103 is a CID containing protein that functions in DNA damage response. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.
Feature 1:CTD binding site [polypeptide binding site]
Evidence:
Comment:based on the interaction site between CTD (C-terminal domain of RNAP II) peptides and CIDs (CTD-Interacting Domain) of human RPRD1A and yeast Rtt103
Structure:4JXT: Human RPRD1A CID in complex with a phosphorylated peptide from RPB1-CTD; contacts at 4A
Jiyao W et al.(2023). "The conserved domain database in 2023.",