1q9y
From Proteopedia
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|PDB= 1q9y |SIZE=350|CAPTION= <scene name='initialview01'>1q9y</scene>, resolution 2.8Å | |PDB= 1q9y |SIZE=350|CAPTION= <scene name='initialview01'>1q9y</scene>, resolution 2.8Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> | + | |LIGAND= <scene name='pdbligand=8OG:8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE'>8OG</scene>, <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=DCP:2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DOC:2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span> |
| - | |GENE= 43 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= | + | |GENE= 43 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12353 Enterobacteria phage RB69]) |
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1q9x|1q9x]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1q9y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q9y OCA], [http://www.ebi.ac.uk/pdbsum/1q9y PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1q9y RCSB]</span> | ||
}} | }} | ||
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==About this Structure== | ==About this Structure== | ||
| - | 1Q9Y is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/ | + | 1Q9Y is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q9Y OCA]. |
==Reference== | ==Reference== | ||
Lesion (in)tolerance reveals insights into DNA replication fidelity., Freisinger E, Grollman AP, Miller H, Kisker C, EMBO J. 2004 Apr 7;23(7):1494-505. Epub 2004 Apr 1. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15057282 15057282] | Lesion (in)tolerance reveals insights into DNA replication fidelity., Freisinger E, Grollman AP, Miller H, Kisker C, EMBO J. 2004 Apr 7;23(7):1494-505. Epub 2004 Apr 1. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15057282 15057282] | ||
[[Category: DNA-directed DNA polymerase]] | [[Category: DNA-directed DNA polymerase]] | ||
| - | [[Category: Enterobacteria phage | + | [[Category: Enterobacteria phage rb69]] |
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Freisinger, E.]] | [[Category: Freisinger, E.]] | ||
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[[Category: Kisker, C.]] | [[Category: Kisker, C.]] | ||
[[Category: Miller, H.]] | [[Category: Miller, H.]] | ||
| - | [[Category: CA]] | ||
| - | [[Category: DCP]] | ||
[[Category: protein_dna complex]] | [[Category: protein_dna complex]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:10:52 2008'' |
Revision as of 20:10, 30 March 2008
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| , resolution 2.8Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , , | ||||||
| Gene: | 43 (Enterobacteria phage RB69) | ||||||
| Activity: | DNA-directed DNA polymerase, with EC number 2.7.7.7 | ||||||
| Related: | 1q9x
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE OF ENTEROBACTERIA PHAGE RB69 GP43 DNA POLYMERASE COMPLEXED WITH 8-OXOGUANOSINE CONTAINING DNA
Overview
The initial encounter of an unrepaired DNA lesion is likely to be with a replicative DNA polymerase, and the outcome of this event determines whether an error-prone or error-free damage avoidance pathway is taken. To understand the atomic details of this critical encounter, we have determined the crystal structures of the pol alpha family RB69 DNA polymerase with DNA containing the two most prevalent, spontaneously generated premutagenic lesions, an abasic site and 2'-deoxy-7,8-dihydro-8-oxoguanosine (8-oxodG). Identification of the interactions between these damaged nucleotides and the active site provides insight into the capacity of the polymerase to incorporate a base opposite the lesion. A novel open, catalytically inactive conformation of the DNA polymerase has been identified in the complex with a primed abasic site template. This structure provides the first molecular characterization of the DNA synthesis barrier caused by an abasic site and suggests a general mechanism for polymerase fidelity. In contrast, the structure of the ternary 8-oxodG:dCTP complex is almost identical to the replicating complex containing unmodified DNA, explaining the relative ease and fidelity by which this lesion is bypassed.
About this Structure
1Q9Y is a Single protein structure of sequence from Enterobacteria phage rb69. Full crystallographic information is available from OCA.
Reference
Lesion (in)tolerance reveals insights into DNA replication fidelity., Freisinger E, Grollman AP, Miller H, Kisker C, EMBO J. 2004 Apr 7;23(7):1494-505. Epub 2004 Apr 1. PMID:15057282
Page seeded by OCA on Sun Mar 30 23:10:52 2008
