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| | <StructureSection load='2vwj' size='340' side='right'caption='[[2vwj]], [[Resolution|resolution]] 2.78Å' scene=''> | | <StructureSection load='2vwj' size='340' side='right'caption='[[2vwj]], [[Resolution|resolution]] 2.78Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2vwj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_700654 Atcc 700654]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VWJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2VWJ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2vwj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_gorgonarius Thermococcus gorgonarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VWJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VWJ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</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]] 2.78Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DU:2-DEOXYURIDINE-5-MONOPHOSPHATE'>DU</scene></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1wn7|1wn7]], [[1tgo|1tgo]], [[2vwk|2vwk]]</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=2vwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vwj OCA], [https://pdbe.org/2vwj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vwj RCSB], [https://www.ebi.ac.uk/pdbsum/2vwj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vwj ProSAT]</span></td></tr> |
| - | <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>
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| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2vwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vwj OCA], [http://pdbe.org/2vwj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vwj RCSB], [http://www.ebi.ac.uk/pdbsum/2vwj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vwj ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DPOL_THEGO DPOL_THEGO]] In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' exonuclease activity. | + | [https://www.uniprot.org/uniprot/DPOL_THEGO DPOL_THEGO] In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' exonuclease activity. |
| | == 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: Atcc 700654]] | |
| - | [[Category: DNA-directed DNA polymerase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Connolly, B A]] | + | [[Category: Thermococcus gorgonarius]] |
| - | [[Category: Firbank, S J]] | + | [[Category: Connolly BA]] |
| - | [[Category: Heslop, P]] | + | [[Category: Firbank SJ]] |
| - | [[Category: Lewis, R J]] | + | [[Category: Heslop P]] |
| - | [[Category: Wardle, J]] | + | [[Category: Lewis RJ]] |
| - | [[Category: Archaea]]
| + | [[Category: Wardle J]] |
| - | [[Category: Dna polymerase]]
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| - | [[Category: Dna repair]]
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| - | [[Category: Dna replication]]
| + | |
| - | [[Category: Dna-binding]]
| + | |
| - | [[Category: Dna-directed dna polymerase]]
| + | |
| - | [[Category: Exonuclease]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Multifunctional enzyme]]
| + | |
| - | [[Category: Nuclease]]
| + | |
| - | [[Category: Nucleotidyltransferase]]
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| - | [[Category: Transferase]]
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| - | [[Category: Uracil]]
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| Structural highlights
Function
DPOL_THEGO In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' exonuclease activity.
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
Archaeal family B DNA polymerases bind tightly to template-strand uracil and stall replication on encountering the pro-mutagenic base. This article describes an X-ray crystal structure, at 2.8 A resolution, of Thermococcus gorgonarius polymerase in complex with a DNA primer-template containing uracil in the single-stranded region. The DNA backbone is distorted to position the uracil deeply within a pocket, located in the amino-terminal domain of the polymerase. Specificity arises from a combination of hydrogen bonds between the protein backbone and uracil, with the pocket shaped to prevent the stable binding of the four standard DNA bases. Strong interactions are seen with the two phosphates that flank the uracil and the structure gives clues concerning the coupling of uracil binding to the halting of replication. The importance of key amino acids, identified by the analysis of the structure and their conservation between archaeal polymerases, was confirmed by site-directed mutagenesis. The crystal structure of V93Q, a polymerase variant that no longer recognises uracil, is also reported, explaining the V93Q phenotype by the steric exclusion of uracil from the pocket.
Uracil recognition in archaeal DNA polymerases captured by X-ray crystallography.,Firbank SJ, Wardle J, Heslop P, Lewis RJ, Connolly BA J Mol Biol. 2008 Sep 5;381(3):529-39. Epub 2008 Jun 7. PMID:18614176[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Firbank SJ, Wardle J, Heslop P, Lewis RJ, Connolly BA. Uracil recognition in archaeal DNA polymerases captured by X-ray crystallography. J Mol Biol. 2008 Sep 5;381(3):529-39. Epub 2008 Jun 7. PMID:18614176 doi:10.1016/j.jmb.2008.06.004
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