1yql
From Proteopedia
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|PDB= 1yql |SIZE=350|CAPTION= <scene name='initialview01'>1yql</scene>, resolution 2.60Å | |PDB= 1yql |SIZE=350|CAPTION= <scene name='initialview01'>1yql</scene>, resolution 2.60Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=CA:CALCIUM ION'>CA</scene> | + | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=PPW:7-DEAZA-8-AZA-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>PPW</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= OGG1, MMH, MUTM, OGH1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]) | |GENE= OGG1, MMH, MUTM, OGH1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1yqk|1YQK]], [[1ebm|1EBM]], [[1yqr|1YQR]], [[1yqm|1YQM]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yql FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yql OCA], [http://www.ebi.ac.uk/pdbsum/1yql PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1yql RCSB]</span> | ||
}} | }} | ||
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==Overview== | ==Overview== | ||
How DNA repair proteins distinguish between the rare sites of damage and the vast expanse of normal DNA is poorly understood. Recognizing the mutagenic lesion 8-oxoguanine (oxoG) represents an especially formidable challenge, because this oxidized nucleobase differs by only two atoms from its normal counterpart, guanine (G). Here we report the use of a covalent trapping strategy to capture a human oxoG repair protein, 8-oxoguanine DNA glycosylase I (hOGG1), in the act of interrogating normal DNA. The X-ray structure of the trapped complex features a target G nucleobase extruded from the DNA helix but denied insertion into the lesion recognition pocket of the enzyme. Free energy difference calculations show that both attractive and repulsive interactions have an important role in the preferential binding of oxoG compared with G to the active site. The structure reveals a remarkably effective gate-keeping strategy for lesion discrimination and suggests a mechanism for oxoG insertion into the hOGG1 active site. | How DNA repair proteins distinguish between the rare sites of damage and the vast expanse of normal DNA is poorly understood. Recognizing the mutagenic lesion 8-oxoguanine (oxoG) represents an especially formidable challenge, because this oxidized nucleobase differs by only two atoms from its normal counterpart, guanine (G). Here we report the use of a covalent trapping strategy to capture a human oxoG repair protein, 8-oxoguanine DNA glycosylase I (hOGG1), in the act of interrogating normal DNA. The X-ray structure of the trapped complex features a target G nucleobase extruded from the DNA helix but denied insertion into the lesion recognition pocket of the enzyme. Free energy difference calculations show that both attractive and repulsive interactions have an important role in the preferential binding of oxoG compared with G to the active site. The structure reveals a remarkably effective gate-keeping strategy for lesion discrimination and suggests a mechanism for oxoG insertion into the hOGG1 active site. | ||
| - | |||
| - | ==Disease== | ||
| - | Known disease associated with this structure: Renal cell carcinoma, clear cell, somatic OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=601982 601982]] | ||
==About this Structure== | ==About this Structure== | ||
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[[Category: Verdine, G L.]] | [[Category: Verdine, G L.]] | ||
[[Category: Yang, W.]] | [[Category: Yang, W.]] | ||
| - | [[Category: CA]] | ||
[[Category: disulfide crosslinking]] | [[Category: disulfide crosslinking]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:18:05 2008'' |
Revision as of 22:18, 30 March 2008
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| , resolution 2.60Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , | ||||||
| Gene: | OGG1, MMH, MUTM, OGH1 (Homo sapiens) | ||||||
| Related: | 1YQK, 1EBM, 1YQR, 1YQM
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Catalytically inactive hOGG1 crosslinked with 7-deaza-8-azaguanine containing DNA
Overview
How DNA repair proteins distinguish between the rare sites of damage and the vast expanse of normal DNA is poorly understood. Recognizing the mutagenic lesion 8-oxoguanine (oxoG) represents an especially formidable challenge, because this oxidized nucleobase differs by only two atoms from its normal counterpart, guanine (G). Here we report the use of a covalent trapping strategy to capture a human oxoG repair protein, 8-oxoguanine DNA glycosylase I (hOGG1), in the act of interrogating normal DNA. The X-ray structure of the trapped complex features a target G nucleobase extruded from the DNA helix but denied insertion into the lesion recognition pocket of the enzyme. Free energy difference calculations show that both attractive and repulsive interactions have an important role in the preferential binding of oxoG compared with G to the active site. The structure reveals a remarkably effective gate-keeping strategy for lesion discrimination and suggests a mechanism for oxoG insertion into the hOGG1 active site.
About this Structure
1YQL is a Single protein structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.
Reference
Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA., Banerjee A, Yang W, Karplus M, Verdine GL, Nature. 2005 Mar 31;434(7033):612-8. PMID:15800616
Page seeded by OCA on Mon Mar 31 01:18:05 2008
