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 . 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 . 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 . 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 .
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