ISDA

Deposition Date 2012-09-05

Release Date 2013-04-17

Last Version Date 2023-12-20

Entry Detail

PDB ID:

4B9M

Keywords:

TRANSFERASE/DNA

Title:

Structure of the high fidelity DNA polymerase I with an oxidative formamidopyrimidine-dA DNA lesion -thymine basepair in the post- insertion site.

Biological Source:

Source Organism:

GEOBACILLUS STEAROTHERMOPHILUS (Taxon ID: 1422)

Host Organism:

ESCHERICHIA COLI

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.05 Å

R-Value Free:

0.22

R-Value Work:

0.18

R-Value Observed:

0.18

Space Group:

P 21 21 21

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA POLYMERASE I
Gene (Uniprot):polA
Chain IDs:A
Chain Length:619
Number of Molecules:1
Biological Source:GEOBACILLUS STEAROTHERMOPHILUS

UniProt ID:E1C9K5 Pfam ID:PF22619, PF00476 EC:2.7.7.49

Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*TP*TP)-3'
Chain IDs:B
Chain Length:11
Number of Molecules:1
Biological Source:GEOBACILLUS STEAROTHERMOPHILUS

Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(*DC*DA*DA*FAX*AP*GP*AP*GP*TP*CP*AP*GP*GP*CP*TP)-3'
Chain IDs:C
Chain Length:15
Number of Molecules:1
Biological Source:GEOBACILLUS STEAROTHERMOPHILUS

Ligand Molecules

SO4

Primary Citation

Unexpected Non-Hoogsteen-Based Mutagenicity Mechanism of Fapy-DNA Lesions.

Gehrke, T.H, Lischke, U, Gasteiger, K.L, Schneider, S, Arnold, S, Muller, H.C, Stephenson, D.S, Zipse, H, Carell, T.Show

Nat.Chem.Biol. 9 455 ? (2013)

PMID: 23685671 DOI: 10.1038/NCHEMBIO.1254

Abstact

8-Oxopurines (8-oxodG and 8-oxodA) and formamidopyrimidines (FaPydG and FaPydA) are major oxidative DNA lesions involved in cancer development and aging. Their mutagenicity is believed to result from a conformational shift of the N9-C1' glycosidic bonds from anti to syn, which allows the lesions to form noncanonical Hoogsteen-type base pairs with incoming triphosphates during DNA replication. Here we present biochemical data and what are to our knowledge the first crystal structures of carbocyclic FaPydA and FaPydG containing DNA in complex with a high-fidelity polymerase. Crystallographic snapshots show that the cFaPy lesions keep the anti geometry of the glycosidic bond during error-free and error-prone replication. The observed dG·dC→dT·dA transversion mutations are the result of base shifting and tautomerization.

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Primary Citation of related structures