PROSITE documentation PDOC51479
Zinc finger RTR1-type profile


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 α 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].

Last update:

April 2016 / Text revised.


Technical section

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

ZF_RTR1, PS51479; RTR1-type zinc finger  (MATRIX)


1AuthorsPhatnani H.P. Greenleaf A.L.
TitlePhosphorylation and functions of the RNA polymerase II CTD.
SourceGenes Dev. 20:2922-2936(2006).
PubMed ID17079683

2AuthorsJeronimo 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.
TitleSystematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme.
SourceMol. Cell 27:262-274(2007).
PubMed ID17643375

3AuthorsMosley A.L. Pattenden S.G. Carey M. Venkatesh S. Gilmore J.M. Florens L. Workman J.L. Washburn M.P.
TitleRtr1 is a CTD phosphatase that regulates RNA polymerase II during the transition from serine 5 to serine 2 phosphorylation.
SourceMol. Cell 34:168-178(2009).
PubMed ID19394294

4AuthorsGibney P.A. Fries T. Bailer S.M. Morano K.A.
TitleRtr1 is the Saccharomyces cerevisiae homolog of a novel family of RNA polymerase II-binding proteins.
SourceEukaryot. Cell 7:938-948(2008).
PubMed ID18408053

5AuthorsXiang K. Manley J.L. Tong L.
TitleThe yeast regulator of transcription protein Rtr1 lacks an active site and phosphatase activity.
SourceNat. Commun. 3:946-946(2012).
PubMed ID22781759

PROSITE is copyrighted by the SIB Swiss Institute of Bioinformatics and distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives (CC BY-NC-ND 4.0) License, see prosite_license.html.


View entry in original PROSITE document format
View entry in raw text format (no links)