ISDA: 6W0M

Deposition Date 2020-03-02

Release Date 2020-09-23

Last Version Date 2023-10-11

Entry Detail

PDB ID:

6W0M

Keywords:

Lyase/DNA

Title:

Human 8-oxoguanine glycosylase crosslinked with oxoG lesion containing DNA

Biological Source:

Source Organism(s):

Homo sapiens (Taxon ID: 9606)

Expression System(s):

Escherichia coli bl21(de3)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.37 Å

R-Value Free:

0.26

R-Value Work:

0.19

R-Value Observed:

0.20

Space Group:

P 65 2 2

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:N-glycosylase/DNA lyase
Gene (Uniprot):OGG1
Mutagens:E122Q, Y207C, K249Q
Chain IDs:A
Chain Length:317
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O15527 Pfam ID:PF07934, PF00730 EC:3.2.2.23

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*C)-3')
Chain IDs:B
Chain Length:13
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3')
Chain IDs:C
Chain Length:15
Number of Molecules:1
Biological Source:Homo sapiens

Ligand Molecules

S5Y

Primary Citation

The trajectory of intrahelical lesion recognition and extrusion by the human 8-oxoguanine DNA glycosylase.

Shigdel, U.K, Ovchinnikov, V, Lee, S.J, Shih, J.A, Karplus, M, Nam, K, Verdine, G.L.Show

Nat Commun 11 4437 4437 (2020)

PMID: 32895378 DOI: 10.1038/s41467-020-18290-2

Abstact

Efficient search for DNA damage embedded in vast expanses of the DNA genome presents one of the greatest challenges to DNA repair enzymes. We report here crystal structures of human 8-oxoguanine (oxoG) DNA glycosylase, hOGG1, that interact with the DNA containing the damaged base oxoG and the normal base G while they are nested in the DNA helical stack. The structures reveal that hOGG1 engages the DNA using different protein-DNA contacts from those observed in the previously determined lesion recognition complex and other hOGG1-DNA complexes. By applying molecular dynamics simulations, we have determined the pathways taken by the lesion and normal bases when extruded from the DNA helix and their associated free energy profiles. These results reveal how the human oxoG DNA glycosylase hOGG1 locates the lesions inside the DNA helix and facilitates their extrusion for repair.

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Protein

Chemical

Disease

Primary Citation of related structures

Abstact

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