3UIQ

RB69 DNA Polymerase Ternary Complex containing dUpNpp

Summary for 3UIQ

• Entry DOI: 10.2210/pdb3uiq/pdb
• Descriptor: DNA polymerase, 5'-D(*TP*CP*GP*AP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3', 5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*C)-3', ... (6 entities in total)
• Functional Keywords: dupnpp, rb69, wt, transferase-dna complex, transferase/dna
• Biological source: Enterobacteria phage RB69
• Total number of polymer chains: 3
• Total formula weight: 114959.96

Authors

Xia, S.,Konigsberg, W.H.,Wang, J. (deposition date: 2011-11-05, release date: 2012-04-18, Last modification date: 2024-02-28)

Primary citation

Xia, S.,Eom, S.H.,Konigsberg, W.H.,Wang, J.
Bidentate and tridentate metal-ion coordination states within ternary complexes of RB69 DNA polymerase.
Protein Sci., 21:447-451, 2012

PubMed Abstract: Two divalent metal ions are required for primer-extension catalyzed by DNA polymerases. One metal ion brings the 3'-hydroxyl of the primer terminus and the α-phosphorus atom of incoming dNTP together for bond formation so that the catalytically relevant conformation of the triphosphate tail of the dNTP is in an α,β,γ-tridentate coordination complex with the second metal ion required for proper substrate alignment. A probable base selectivity mechanism derived from structural studies on Dpo4 suggests that the inability of mispaired dNTPs to form a substrate-aligned, tridentate coordination complex could effectively cause the mispaired dNTPs to be rejected before catalysis. Nevertheless, we found that mispaired dNTPs can actually form a properly aligned tridentate coordination complex. However, complementary dNTPs occasionally form misaligned complexes with mutant RB69 DNA polymerases (RB69pols) that are not in a tridentate coordination state. Here, we report finding a β,γ-bidentate coordination complex that contained the complementary dUpNpp opposite dA in the structure of a ternary complex formed by the wild type RB69pol at 1.88 Å resolution. Our observations suggest that several distinct metal-ion coordination states can exist at the ground state in the polymerase active site and that base selectivity is unlikely to be based on metal-ion coordination alone.

PubMed: 22238207
DOI: 10.1002/pro.2026

Experimental method

X-RAY DIFFRACTION (1.879 Å)