ISDA

Entry Detail

PDB ID:

4B9U

Keywords:

Title:

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

Biological Source:

Source Organism:

GEOBACILLUS STEAROTHERMOPHILUS

Host Organism:

ESCHERICHIA COLI

PDB Version:

Deposition Date:

2012-09-06

Release Date:

2013-04-17

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.10 Å

R-Value Free:

0.22

R-Value Work:

0.19

R-Value Observed:

0.19

Space Group:

P 21 21 21

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Macromolecular Entities

Protein Blast

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

Polymer Type:polydeoxyribonucleotide
Description:5'-D(*CP*AP*AP*FOXP*CP*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

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
FOX	C	DG	?

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