Crystal Structure of Yeast DNA Polymerase ε Catalytic Domain (original) (raw)
Figure 3
Comparison between the Pol2G:C and Pol2T:A polymerase and exonuclease active sites.
(a) The nascent base pair binding pocket is shaped by residues Val825 (not shown for clarity), Asn828, Ser829, Ty831 and Gly832 from the fingers domain, and by Tyr645 from the palm domain. Tyr431 approaches the incoming nucleotide from the major groove side. Contacts to the G:C and T:A base pairs are interchangeable in the two structures. (b) The polymerase active site is characterized by acidic residues Asp640 and Asp877. The Pol2G:C (this work) structure has two Ca2+ ions (gray spheres) at positions A and B in the polymerase active site. Pol2T:A structure was crystallized with one Mg2+ ion in the active site. (c) Exonuclease active site in Pol2GC (left) and Pol2TA (right). Ca2+ ion at position B of Pol2G:C is shown as gray sphere and is coordinated by Asp290, and a water molecule (red sphere). The atom at position A was modeled as water due to its close proximity to the metal ion at position B. In the Pol2T:A structure, the exonuclease catalytic residues (Asp290 and Glu292) were mutated to alanines and there are no bound metal ions.