PDBsum entry 3raq

Transferase/DNA

PDB id: 3raq

Contents

Protein chains

341 a.a.

DNA/RNA

Ligands

DGT ×2

EPE ×2

Metals

_CA ×6

Waters ×298

PDB id:

3raq

Name:

Transferase/DNA

Title:

Dpo4 extension ternary complex with 3'-terminal primer c base opposite the 1-methylguanine (mg1) lesion

Structure:

DNA polymerase iv. Chain: a, b. Synonym: pol iv. Engineered: yes. DNA (5'-d( Gp Tp Tp Gp Gp Ap Tp Gp Gp Tp Ap Gp (Doc))-3'). Chain: d, h. Engineered: yes. Other_details: DNA primer strand (dideoxy-terminated at the 3-end). DNA (5'-d( C Cp Tp Ap Ap Cp (Mg1)

Source:

Sulfolobus solfataricus. Organism_taxid: 2287. Strain: p2. Gene: dbh, dpo4, sso2448. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Other_details: synthetic. Other_details: synthetic

Resolution:

2.25Å R-factor: 0.196 R-free: 0.235

Authors:

O.Rechkoblit,D.J.Patel

Key ref:

O.Rechkoblit et al. (2011). Implications for damage recognition during Dpo4-mediated mutagenic bypass of m1G and m3C lesions. Structure, 19, 821-832. PubMed id: 21645853

Date:

28-Mar-11 Release date: 15-Jun-11

Protein chains

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.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

G-T-T-G-G-A-T-G-G-T-A-G-DOC 13 bases

T-A-A-C-MG1-C-T-A-C-C-A-T-C-C-A-A-C-C 18 bases

G-T-T-G-G-A-T-G-G-T-A-G-DOC 13 bases

A-A-C-MG1-C-T-A-C-C-A-T-C-C-A-A-C-C 17 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

Structure 19:821-832 (2011)

PubMed id: 21645853

Implications for damage recognition during Dpo4-mediated mutagenic bypass of m1G and m3C lesions.

O.Rechkoblit, J.C.Delaney, J.M.Essigmann, D.J.Patel.

ABSTRACT

DNA is susceptible to alkylation damage by a number of environmental agents that modify the Watson-Crick edge of the bases. Such lesions, if not repaired, may be bypassed by Y-family DNA polymerases. The bypass polymerase Dpo4 is strongly inhibited by 1-methylguanine (m1G) and 3-methylcytosine (m3C), with nucleotide incorporation opposite these lesions being predominantly mutagenic. Further, extension after insertion of both correct and incorrect bases, introduces additional base substitution and deletion errors. Crystal structures of the Dpo4 ternary extension complexes with correct and mismatched 3'-terminal primer bases opposite the lesions reveal that both m1G and m3C remain positioned within the DNA template/primer helix. However, both correct and incorrect pairing partners exhibit pronounced primer terminal nucleotide distortion, being primarily evicted from the DNA helix when opposite m1G or misaligned when pairing with m3C. Our studies provide insights into mechanisms related to hindered and mutagenic bypass of methylated lesions and models associated with damage recognition by repair demethylases.