{PDOC51391}
{PS51391; CID}
{BEGIN}
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* CID domain profile *
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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 alpha-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.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: June 2008 / First entry.

[ 1] Meinhart A., Cramer P.
     "Recognition of RNA polymerase II carboxy-terminal domain by
     3'-RNA-processing factors."
     Nature 430:223-226(2004).
     PubMed=15241417; DOI=10.1038/nature02679
[ 2] Noble C.G., Hollingworth D., Martin S.R., Ennis-Adeniran V.,
     Smerdon S.J., Kelly G., Taylor I.A., Ramos A.
     "Key features of the interaction between Pcf11 CID and RNA polymerase
     II CTD."
     Nat. Struct. Mol. Biol. 12:144-151(2005).
     PubMed=15665873; DOI=10.1038/nsmb887

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