4O9M image
Deposition Date 2014-01-02
Release Date 2014-04-30
Last Version Date 2023-09-20
Entry Detail
PDB ID:
4O9M
Keywords:
TRANSFERASE/DNA
Title:
Human DNA polymerase beta complexed with adenylated tetrahydrofuran (abasic site) containing DNA
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.30 Å
R-Value Free:
0.26
R-Value Work:
0.19
R-Value Observed:
0.20
Space Group:
P 1 21 1
4O9M validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA polymerase beta
Gene (Uniprot):POLB
Chain IDs:D (auth: 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
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
Chain IDs:A (auth: B)
Chain Length:16
Number of Molecules:1
Biological Source:
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*C)-3')
Chain IDs:B (auth: C)
Chain Length:11
Number of Molecules:1
Biological Source:
Polymer Type:polydeoxyribonucleotide/polyribonucleotide hybrid
Molecule:(5'-D(P*GP*TP*CP*GP*G)-3');
Chain IDs:C (auth: D)
Chain Length:5
Number of Molecules:1
Biological Source:
Ligand Molecules
2RW
NA
Primary Citation
Role of polymerase beta in complementing aprataxin deficiency during abasic-site base excision repair.
Nat.Struct.Mol.Biol. 21 497 499 (2014)
PMID: 24777061 DOI: 10.1038/nsmb.2818

Abstact

DNA polymerase β (pol β) lyase removal of 5'-deoxyribose phosphate (5'-dRP) from base excision repair (BER) intermediates is critical in mammalian BER involving the abasic site. We found that pol β also removes 5'-adenylated dRP from BER intermediates after abortive ligation. The crystal structure of a human pol β-DNA complex showed the 5'-AMP-dRP group positioned in the lyase active site. Pol β expression rescued methyl methanesulfonate sensitivity in aprataxin (hnt3)- and FEN1 (rad27)-deficient yeast.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
4O9M