2p5o: Difference between revisions
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|PDB= 2p5o |SIZE=350|CAPTION= <scene name='initialview01'>2p5o</scene>, resolution 2.8Å | |PDB= 2p5o |SIZE=350|CAPTION= <scene name='initialview01'>2p5o</scene>, resolution 2.8Å | ||
|SITE= | |SITE= | ||
|LIGAND= | |LIGAND= <scene name='pdbligand=3DR:1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE'>3DR</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=MSE:SELENOMETHIONINE'>MSE</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=[[1ig9|1IG9]], [[1clq|1CLQ]], [[2dy4|2DY4]], [[2dtu|2DTU]], [[1q9y|1Q9Y]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2p5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p5o OCA], [http://www.ebi.ac.uk/pdbsum/2p5o PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2p5o RCSB]</span> | |||
}} | }} | ||
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==About this Structure== | ==About this Structure== | ||
2P5O is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/ | 2P5O is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]. This structure supersedes the now removed PDB entry 1RV2. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P5O OCA]. | ||
==Reference== | ==Reference== | ||
Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site., Hogg M, Wallace SS, Doublie S, EMBO J. 2004 Apr 7;23(7):1483-93. Epub 2004 Apr 1. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15057283 15057283] | Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site., Hogg M, Wallace SS, Doublie S, EMBO J. 2004 Apr 7;23(7):1483-93. Epub 2004 Apr 1. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15057283 15057283] | ||
[[Category: DNA-directed DNA polymerase]] | [[Category: DNA-directed DNA polymerase]] | ||
[[Category: Enterobacteria phage | [[Category: Enterobacteria phage rb69]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Doublie, S.]] | [[Category: Doublie, S.]] | ||
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[[Category: exonuclease switch]] | [[Category: exonuclease switch]] | ||
''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 04:30:05 2008'' | ||
Revision as of 04:30, 31 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: | 1IG9, 1CLQ, 2DY4, 2DTU, 1Q9Y
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of RB69 GP43 in complex with DNA containing an abasic site analog
OverviewOverview
Abasic sites are common DNA lesions, which are strong blocks to replicative polymerases and are potentially mutagenic when bypassed. We report here the 2.8 A structure of the bacteriophage RB69 replicative DNA polymerase attempting to process an abasic site analog. Four different complexes were captured in the crystal asymmetric unit: two have DNA in the polymerase active site whereas the other two molecules are in the exonuclease mode. When compared to complexes with undamaged DNA, the DNA surrounding the abasic site reveals distinct changes suggesting why the lesion is so poorly bypassed: the DNA in the polymerase active site has not translocated and is therefore stalled, precluding extension. All four molecules exhibit conformations that differ from the previously published structures. The polymerase incorporates dAMP across the lesion under crystallization conditions, indicating that the different conformations observed in the crystal may be part of the active site switching reaction pathway.
About this StructureAbout this Structure
2P5O is a Single protein structure of sequence from Enterobacteria phage rb69. This structure supersedes the now removed PDB entry 1RV2. Full crystallographic information is available from OCA.
ReferenceReference
Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site., Hogg M, Wallace SS, Doublie S, EMBO J. 2004 Apr 7;23(7):1483-93. Epub 2004 Apr 1. PMID:15057283
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