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].