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| | <StructureSection load='1q9y' size='340' side='right'caption='[[1q9y]], [[Resolution|resolution]] 2.80Å' scene=''> | | <StructureSection load='1q9y' size='340' side='right'caption='[[1q9y]], [[Resolution|resolution]] 2.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1q9y]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpr69 Bpr69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q9Y OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1Q9Y FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1q9y]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_RB69 Escherichia phage RB69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q9Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q9Y FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1q9x|1q9x]]</div></td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1q9y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q9y OCA], [https://pdbe.org/1q9y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q9y RCSB], [https://www.ebi.ac.uk/pdbsum/1q9y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q9y ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">43 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12353 BPR69])</td></tr>
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| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1q9y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q9y OCA], [http://pdbe.org/1q9y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q9y RCSB], [http://www.ebi.ac.uk/pdbsum/1q9y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1q9y ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DPOL_BPR69 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. | + | [https://www.uniprot.org/uniprot/DPOL_BPR69 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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bpr69]] | + | [[Category: Escherichia phage RB69]] |
| - | [[Category: DNA-directed DNA polymerase]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Freisinger, E]] | + | [[Category: Freisinger E]] |
| - | [[Category: Grollman, A P]] | + | [[Category: Grollman AP]] |
| - | [[Category: Kisker, C]] | + | [[Category: Kisker C]] |
| - | [[Category: Miller, H]] | + | [[Category: Miller H]] |
| - | [[Category: Protein_dna complex]]
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| - | [[Category: Replication-dna complex]]
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| - | [[Category: Transferase]]
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| Structural highlights
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
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Freisinger E, Grollman AP, Miller H, Kisker C. Lesion (in)tolerance reveals insights into DNA replication fidelity. EMBO J. 2004 Apr 7;23(7):1494-505. Epub 2004 Apr 1. PMID:15057282 doi:http://dx.doi.org/10.1038/sj.emboj.7600158
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