9ICP

DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF PYROPHOSPHATE (1 MILLIMOLAR) AND MGCL2 (5 MILLIMOLAR)

Summary for 9ICP

• Entry DOI: 10.2210/pdb9icp/pdb
• Related: 1ZQA 1ZQB 1ZQC 1ZQD 1ZQE 1ZQF 1ZQG 1ZQH 1ZQI 1ZQJ 1ZQK 1ZQL 1ZQM 1ZQN 1ZQO 1ZQP 1ZQQ 1ZQR 1ZQS 1ZQT 7ICE 7ICF 7ICG 7ICH 7ICI 7ICJ 7ICK 7ICL 7ICM 7ICN 7ICO 7ICP 7ICQ 7ICR 7ICS 7ICT 7ICU 7ICV 8ICA 8ICB 8ICC 8ICE 8ICF 8ICG 8ICH 8ICI 8ICJ 8ICK 8ICL 8ICM 8ICN 8ICO 8ICP 8ICQ 8ICR 8ICS 8ICT 8ICU 8ICV 8ICW 8ICX 8ICY 8ICZ 9ICA 9ICB 9ICC 9ICE 9ICF 9ICG 9ICH 9ICI 9ICJ 9ICK 9ICL 9ICM 9ICN 9ICO 9ICQ 9ICR 9ICS 9ICT 9ICU 9ICV 9ICW 9ICX 9ICY
• Descriptor: DNA (5'-D(*CP*AP*TP*CP*TP*GP*T)-3'), DNA (5'-D(*CP*AP*GP*AP*TP*G)-3'), PROTEIN (DNA POLYMERASE BETA (E.C.2.7.7.7)), ... (5 entities in total)
• Functional Keywords: dna-directed dna polymerase, dna replication, dna repair, nucleotidyltransferase, complex (nucleotidyltransferase-dna, transferase-dna complex, transferase/dna
• Biological source: Homo sapiens (human)
• Cellular location: Nucleus: P06746
• Total number of polymer chains: 3
• Total formula weight: 42209.29

Authors

Pelletier, H.,Sawaya, M.R. (deposition date: 1995-12-16, release date: 1996-11-15, Last modification date: 2023-08-02)

Primary citation

Pelletier, H.,Sawaya, M.R.,Wolfle, W.,Wilson, S.H.,Kraut, J.
A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta
Biochemistry, 35:12762-12777, 1996

PubMed Abstract: When crystals of human DNA polymerase beta (pol beta) complexed with DNA [Pelletier, H., Sawaya, M. R., Wolfle, W., Wilson, S. H., & Kraut, J. (1996) Biochemistry 35, 12742-12761] are soaked in the presence of dATP and Mn2+, X-ray structural analysis shows that nucleotidyl transfer to the primer 3'-OH takes place directly in the crystals, even though the DNA is blunt-ended at the active site. Under similar crystal-soaking conditions, there is no evidence for a reaction when Mn2+ is replaced by Mg2+, which is thought to be the divalent metal ion utilized by most polymerases in vivo. These results suggest that one way Mn2+ may manifest its mutagenic effect on polymerases is by promoting greater reactivity than Mg2+ at the catalytic site, thereby allowing the nucleotidyl transfer reaction to take place with little or no regard to instructions from a template. Non-template-directed nucleotidyl transfer is also observed when pol beta-DNA cocrystals are soaked in the presence of dATP and Zn2+, but the reaction products differ in that the sugar moiety of the incorporated nucleotide appears distorted or otherwise cleaved, in agreement with reports that Zn2+ may act as a polymerase inhibitor rather than as a mutagen [Sirover, M. A., & Loeb, L. A. (1976) Science 194, 1434-1436]. Although no reaction is observed when crystals are soaked in the presence of dATP and other metal ions such as Ca2+, Co2+, Cr3+, or Ni2+, X-ray structural analyses show that these metal ions coordinate the triphosphate moiety of the nucleotide in a manner that differs from that observed with Mg2+. In addition, all metal ions tested, with the exception of Mg2+, promote a change in the side-chain position of aspartic acid 192, which is one of three highly conserved active-site carboxylate residues. Soaking experiments with nucleotides other than dATP (namely, dCTP, dGTP, dTTP, ATP, ddATP, ddCTP, AZT-TP, and dATP alpha S) reveal a non-base-specific binding site on pol beta for the triphosphate and sugar moieties of a nucleotide, suggesting a possible mechanism for nucleotide selectivity whereby triphosphate-sugar binding precedes a check for correct base pairing with the template.

PubMed: 8841119
DOI: 10.1021/bi9529566

Experimental method

X-RAY DIFFRACTION (3.1 Å)