3MBY image
Deposition Date 2010-03-26
Release Date 2010-06-09
Last Version Date 2023-09-06
Entry Detail
PDB ID:
3MBY
Keywords:
Transferase, Lyase/DNA
Title:
Ternary complex of DNA Polymerase BETA with template base A and 8oxodGTP in the active site with a dideoxy terminated primer
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.00 Å
R-Value Free:
0.24
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 1 21 1
3MBY validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA polymerase beta
Gene (Uniprot):POLB
Chain IDs:A
Chain Length:335
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P06746 Pfam ID:PF14716, PF10391, PF14792, PF14791 EC:2.7.7.7
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
DOC C DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
Ligand Molecules
8DG
CL
MG
NA
Primary Citation
Mutagenic conformation of 8-oxo-7,8-dihydro-2'-dGTP in the confines of a DNA polymerase active site.
Nat.Struct.Mol.Biol. 17 889 890 (2010)
PMID: 20526335 DOI: 10.1038/nsmb.1852

Abstact

The major product of oxidative base damage is 8-oxo-7,8-dihydro-2'-deoxyguanine (8odG). The coding potential of this lesion is modulated by its glycosidic torsion angle that controls whether its Watson-Crick or Hoogsteen edge is used for base pairing. The 2.0-A structure of DNA polymerase (pol) beta bound with 8odGTP opposite template adenine indicates that the modified nucleotide assumes the mutagenic syn conformation and that the nonmutagenic anti conformation would be incompatible with efficient DNA synthesis.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
3MBY