{PDOC51479}
{PS51479; ZF_RTR1}
{BEGIN}
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* Zinc finger RTR1-type profile *
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Proper  RNA processing involves the recruitment of a wide variety of accessory
proteins  to  the  C-terminal  domain  (CTD)  of  the  largest  subunit of RNA
polymerase II (RNAPII), Rpb1 [1]. One regulatory mechanism involves reversible
phosphorylation of the C-terminal domain within RNAPII. The eukaryotic protein
family  Rtr1/RPAP2  interacts with the CTD of RNAPII [2]. It has been shown in
yeast  that  Rtr1  is  a  CTD  phosphatase  that  regulates  RNAPII during the
transition from serine 5 to serine 2 phosphorylation [3]. In addition to Rtr1,
the  phosphatases Ssu72 and Fcp1 (see <PDOC50969>) also play an important role
in the  regulation  of CTD phosphorylation. Rtr1 proteins are poorly conserved
overall, but they share a motif with three strictly conserved Cys residues and
another residue  conserved  as  His  (in most fungi) or Cys (in animals and S.
pombe), suggestive  of a zinc finger motif (C-x(4)-C-x(n)-C-x(3)-[CH], where n
ranges from 30 to 50) [4,5].

The RTR1-type  zinc  finger   is made of two alpha helices connected by a long
loop and  the  three  strictly conserved Cys residues are located in this loop
(see <PDB:4FC8>).  The  fourth  ligand  of  the zinc ion, His or Cys is in the
first turn  of  the second helix. The zinc ion is coordinated in a tetrahedral
fashion by  the  four  conserved  ligands  and probably has a structural role,
likely stabilizing the overall structure of the protein [5].

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: April 2016 / Text revised.

[ 1] Phatnani H.P., Greenleaf A.L.
     "Phosphorylation and functions of the RNA polymerase II CTD."
     Genes Dev. 20:2922-2936(2006).
     PubMed=17079683; DOI=10.1101/gad.1477006
[ 2] Jeronimo C., Forget D., Bouchard A., Li Q., Chua G., Poitras C.,
     Therien C., Bergeron D., Bourassa S., Greenblatt J., Chabot B.,
     Poirier G.G., Hughes T.R., Blanchette M., Price D.H., Coulombe B.
     "Systematic analysis of the protein interaction network for the human
     transcription machinery reveals the identity of the 7SK capping
     enzyme."
     Mol. Cell 27:262-274(2007).
     PubMed=17643375; DOI=10.1016/j.molcel.2007.06.027
[ 3] Mosley A.L., Pattenden S.G., Carey M., Venkatesh S., Gilmore J.M.,
     Florens L., Workman J.L., Washburn M.P.
     "Rtr1 is a CTD phosphatase that regulates RNA polymerase II during the
     transition from serine 5 to serine 2 phosphorylation."
     Mol. Cell 34:168-178(2009).
     PubMed=19394294; DOI=10.1016/j.molcel.2009.02.025
[ 4] Gibney P.A., Fries T., Bailer S.M., Morano K.A.
     "Rtr1 is the Saccharomyces cerevisiae homolog of a novel family of RNA
     polymerase II-binding proteins."
     Eukaryot. Cell 7:938-948(2008).
     PubMed=18408053; DOI=10.1128/EC.00042-08
[ 5] Xiang K., Manley J.L., Tong L.
     "The yeast regulator of transcription protein Rtr1 lacks an active
     site and phosphatase activity."
     Nat. Commun. 3:946-946(2012).
     PubMed=22781759; DOI=10.1038/ncomms1947

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