2p5o

Crystal structure of RB69 GP43 in complex with DNA containing an abasic site analog

spinqualitylabelsall models 2p5o, resolution 2.80Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 2p5o is a 12 chain structure with sequence from Bpr69. This structure supersedes the now removed PDB entry 1rv2. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. NonStd Res: 3DR, MSE Related: 1ig9, 1clq, 2dy4, 2dtu, 1q9y Gene: 43 (BPR69) Activity: DNA-directed DNA polymerase, with EC number 2.7.7.7 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [DPOL_BPR69] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed 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. 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 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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