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| | <StructureSection load='1u4b' size='340' side='right'caption='[[1u4b]], [[Resolution|resolution]] 1.60Å' scene=''> | | <StructureSection load='1u4b' size='340' side='right'caption='[[1u4b]], [[Resolution|resolution]] 1.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1u4b]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U4B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U4B FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1u4b]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U4B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U4B FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</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]] 1.6Å</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></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=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PRD_900003:sucrose'>PRD_900003</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1u45|1u45]], [[1u47|1u47]], [[1u48|1u48]], [[1u49|1u49]]</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=1u4b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u4b OCA], [https://pdbe.org/1u4b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1u4b RCSB], [https://www.ebi.ac.uk/pdbsum/1u4b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1u4b 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>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1u4b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u4b OCA], [http://pdbe.org/1u4b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u4b RCSB], [http://www.ebi.ac.uk/pdbsum/1u4b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1u4b ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DPO1_GEOSE DPO1_GEOSE]] In addition to polymerase activity, this DNA polymerase exhibits 5' to 3' exonuclease activity. | + | [https://www.uniprot.org/uniprot/DPO1_GEOSE DPO1_GEOSE] In addition to polymerase activity, this DNA polymerase exhibits 5' to 3' 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 12980]] | + | [[Category: Geobacillus stearothermophilus]] |
| - | [[Category: DNA-directed DNA polymerase]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Beese, L S]] | + | [[Category: Beese LS]] |
| - | [[Category: Carell, T]] | + | [[Category: Carell T]] |
| - | [[Category: Hsu, G W]] | + | [[Category: Hsu GW]] |
| - | [[Category: Ober, M]] | + | [[Category: Ober M]] |
| - | [[Category: Dna lesion]]
| + | |
| - | [[Category: Dna polymerase i]]
| + | |
| - | [[Category: Dna replication]]
| + | |
| - | [[Category: Klenow fragment]]
| + | |
| - | [[Category: Protein-dna complex]]
| + | |
| - | [[Category: Transferase-dna complex]]
| + | |
| - | [[Category: Translation replication]]
| + | |
| Structural highlights
1u4b is a 3 chain structure with sequence from Geobacillus stearothermophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.6Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
DPO1_GEOSE In addition to polymerase activity, this DNA polymerase exhibits 5' to 3' 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
Aerobic respiration generates reactive oxygen species that can damage guanine residues and lead to the production of 8-oxoguanine (8oxoG), the major mutagenic oxidative lesion in the genome. Oxidative damage is implicated in ageing and cancer, and its prevalence presents a constant challenge to DNA polymerases that ensure accurate transmission of genomic information. When these polymerases encounter 8oxoG, they frequently catalyse misincorporation of adenine in preference to accurate incorporation of cytosine. This results in the propagation of G to T transversions, which are commonly observed somatic mutations associated with human cancers. Here, we present sequential snapshots of a high-fidelity DNA polymerase during both accurate and mutagenic replication of 8oxoG. Comparison of these crystal structures reveals that 8oxoG induces an inversion of the mismatch recognition mechanisms that normally proofread DNA, such that the 8oxoG.adenine mismatch mimics a cognate base pair whereas the 8oxoG.cytosine base pair behaves as a mismatch. These studies reveal a fundamental mechanism of error-prone replication and show how 8oxoG, and DNA lesions in general, can form mismatches that evade polymerase error-detection mechanisms, potentially leading to the stable incorporation of lethal mutations.
Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase.,Hsu GW, Ober M, Carell T, Beese LS Nature. 2004 Sep 9;431(7005):217-21. Epub 2004 Aug 22. PMID:15322558[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Hsu GW, Ober M, Carell T, Beese LS. Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase. Nature. 2004 Sep 9;431(7005):217-21. Epub 2004 Aug 22. PMID:15322558 doi:10.1038/nature02908
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