PDBsum entry 2r8h

Replication, transferase/DNA

PDB id: 2r8h

Contents

Protein chain

341 a.a. *

DNA/RNA

Ligands

DGT

Metals

_CA ×3

Waters ×98

* Residue conservation analysis

PDB id:

2r8h

Name:

Replication, transferase/DNA

Title:

Selectivity of nucleoside triphosphate incorporation opposite 1,n2- propanodeoxyguanosine (pdg) by the sulfolobus solfataricus DNA polymerase dpo4 polymerase

Structure:

DNA (5'- d( Dgp Dgp Dgp Dgp Dgp Dap Dap Dgp Dgp Dap Dtp Dtp Dc)-3'). Chain: p. Engineered: yes. DNA (5'-d( Dtp Dcp Dap Dcp (P) p Dgp Dap Dap Dtp Dcp Dcp Dtp Dtp Dcp Dcp Dcp Dcp Dc)-3'). Chain: t. Engineered: yes. DNA polymerase iv.

Source:

Synthetic: yes. Sulfolobus solfataricus. Organism_taxid: 2287. Gene: dbh, dpo4. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: purified using heat denaturation, ni2+-nitriloacetate chromatography, and ion-exchange chromatography

Resolution:

2.48Å R-factor: 0.215 R-free: 0.279

Authors:

Y.Wang,S.Saleh,L.J.Marnette,M.Egli,M.P.Stone

Key ref:

Y.Wang et al. (2008). Insertion of dNTPs opposite the 1,N2-propanodeoxyguanosine adduct by Sulfolobus solfataricus P2 DNA polymerase IV. Biochemistry, 47, 7322-7334. PubMed id: 18563918

Date:

10-Sep-07 Release date: 22-Jul-08

Protein chain

Q97W02  (DPO4_SULSO) -  DNA polymerase IV from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

Seq: 352 a.a.

Struc: 341 a.a.

DNA/RNA chains

G-G-G-G-G-A-A-G-G-A-T-T-C 13 bases

T-C-A-C-__P-G-A-A-T-C-C-T-T-C-C-C-C-C 18 bases

Enzyme reactions

• Enzyme class: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

Biochemistry 47:7322-7334 (2008)

PubMed id: 18563918

Insertion of dNTPs opposite the 1,N2-propanodeoxyguanosine adduct by Sulfolobus solfataricus P2 DNA polymerase IV.

Y.Wang, S.K.Musser, S.Saleh, L.J.Marnett, M.Egli, M.P.Stone.

ABSTRACT

1, N (2)-Propanodeoxyguanosine (PdG) is a stable structural analogue for the 3-(2'-deoxy-beta- d- erythro-pentofuranosyl)pyrimido[1,2-alpha]purin-10(3 H)-one (M 1dG) adduct derived from exposure of DNA to base propenals and to malondialdehyde. The structures of ternary polymerase-DNA-dNTP complexes for three template-primer DNA sequences were determined, with the Y-family Sulfolobus solfataricus DNA polymerase IV (Dpo4), at resolutions between 2.4 and 2.7 A. Three template 18-mer-primer 13-mer sequences, 5'-d(TCACXAAATCCTTCCCCC)-3'.5'-d(GGGGGAAGGATTT)-3' (template I), 5'-d(TCACXGAATCCTTCCCCC)-3'.5'-d(GGGGGAAGGATTC)-3' (template II), and 5'-d(TCATXGAATCCTTCCCCC)-3'.5'-d(GGGGGAAGGATTC)-3' (template III), where X is PdG, were analyzed. With templates I and II, diffracting ternary complexes including dGTP were obtained. The dGTP did not pair with PdG, but instead with the 5'-neighboring template dC, utilizing Watson-Crick geometry. Replication bypass experiments with the template-primer 5'-TCACXAAATCCTTACGAGCATCGCCCCC-3'.5'-GGGGGCGATGCTCGTAAGGATTT-3', where X is PdG, which includes PdG in the 5'-CXA-3' template sequence as in template I, showed that the Dpo4 polymerase inserted dGTP and dATP when challenged by the PdG adduct. For template III, in which the template sequence was 5'-TXG-3', a diffracting ternary complex including dATP was obtained. The dATP did not pair with PdG, but instead with the 5'-neighboring T, utilizing Watson-Crick geometry. Thus, all three ternary complexes were of the "type II" structure described for ternary complexes with native DNA [Ling, H., Boudsocq, F., Woodgate, R., and Yang, W. (2001) Cell 107, 91-102]. The PdG adduct remained in the anti conformation about the glycosyl bond in each of these threee ternary complexes. These results provide insight into how -1 frameshift mutations might be generated for the PdG adduct, a structural model for the exocylic M 1dG adduct formed by malondialdehyde.