2p5o: Difference between revisions

Revision as of 12:25, 4 May 2008

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 Page seeded by OCA on Sun May 4 12:25:10 2008

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OCA

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 [[Image:2p5o.jpg|left|200px]]
- {{Structure
+<!--
-|PDB= 2p5o |SIZE=350|CAPTION= <scene name='initialview01'>2p5o</scene>, resolution 2.8&Aring;
+The line below this paragraph, containing "STRUCTURE_2p5o", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=3DR:1&#39;,2&#39;-DIDEOXYRIBOFURANOSE-5&#39;-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|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>
+or leave the SCENE parameter empty for the default display.
-|GENE= 43 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12353 Enterobacteria phage RB69])
+-->
-|DOMAIN=
+{{STRUCTURE_2p5o|  PDB=2p5o  |  SCENE=  }}
-|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>
-}}
 '''Crystal structure of RB69 GP43 in complex with DNA containing an abasic site analog'''
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 ==About this Structure==
-P5O 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].
+P5O 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 [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rv2 1rv2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P5O OCA].
 ==Reference==
@@ Line 29: / Line 26: @@
 [[Category: Hogg, M.]]
 [[Category: Wallace, S S.]]
-[[Category: abasic site]]
+[[Category: Abasic site]]
-[[Category: dna lesion]]
+[[Category: Dna lesion]]
-[[Category: dna polymerase]]
+[[Category: Dna polymerase]]
-[[Category: exonuclease switch]]
+[[Category: Exonuclease switch]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 12:25:10 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:30:05 2008''