PDBsum entry 4ruc

Transferase/DNA

PDB id: 4ruc

Contents

Protein chain

341 a.a.

DNA/RNA

Ligands

DTP

Metals

_CA ×3

Waters ×58

PDB id:

4ruc

Name:

Transferase/DNA

Title:

Crystal structure of y-family DNA polymerase dpo4 extending from a mefapy-dg:dc pair

Structure:

DNA polymerase iv. Chain: a. Synonym: pol iv. Engineered: yes. Nucleic acids template: tcat(mf7)taatccttccccc. Chain: t. Engineered: yes. Nucleic acids primar: gggggaaggattac. Chain: p.

Source:

Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: atcc 35092 / dsm 1617 / jcm 11322 / p2. Gene: dbh, dpo4, sso2448. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630.

Resolution:

2.90Å R-factor: 0.175 R-free: 0.236

Authors:

A.Patra,S.Banerjee,M.P.Stone,M.Egli

Key ref:

A.Patra et al. (2015). Structural Basis for Error-Free Bypass of the 5-N-Methylformamidopyrimidine-dG Lesion by Human DNA Polymerase η and Sulfolobus solfataricus P2 Polymerase IV. J Am Chem Soc, 137, 7011-7014. PubMed id: 25988947 DOI: 10.1021/jacs.5b02701

Date:

18-Nov-14 Release date: 05-Aug-15

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

C-A-T-MF7-T-A-A-T-C-C-T-T-C-C-C-C-C 17 bases

G-G-G-G-G-A-A-G-G-A-T-T-A-C 14 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

DOI no: 10.1021/jacs.5b02701

J Am Chem Soc 137:7011-7014 (2015)

PubMed id: 25988947

Structural Basis for Error-Free Bypass of the 5-N-Methylformamidopyrimidine-dG Lesion by Human DNA Polymerase η and Sulfolobus solfataricus P2 Polymerase IV.

A.Patra, S.Banerjee, T.L.Johnson Salyard, C.K.Malik, P.P.Christov, C.J.Rizzo, M.P.Stone, M.Egli.

ABSTRACT

N(6)-(2-Deoxy-d-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine (MeFapy-dG) arises from N7-methylation of deoxyguanosine followed by imidazole ring opening. The lesion has been reported to persist in animal tissues. Previous in vitro replication bypass investigations of the MeFapy-dG adduct revealed predominant insertion of C opposite the lesion, dependent on the identity of the DNA polymerase (Pol) and the local sequence context. Here we report crystal structures of ternary Pol·DNA·dNTP complexes between MeFapy-dG-adducted DNA template:primer duplexes and the Y-family polymerases human Pol η and P2 Pol IV (Dpo4) from Sulfolobus solfataricus. The structures of the hPol η and Dpo4 complexes at the insertion and extension stages, respectively, are representative of error-free replication, with MeFapy-dG in the anti conformation and forming Watson-Crick pairs with dCTP or dC.