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| | <StructureSection load='4b9n' size='340' side='right'caption='[[4b9n]], [[Resolution|resolution]] 2.20Å' scene=''> | | <StructureSection load='4b9n' size='340' side='right'caption='[[4b9n]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4b9n]] 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=4B9N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4B9N FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4b9n]] 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=4B9N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4B9N 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]] 2.2Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAX:[(1R,2S,4R)-4-{[6-AMINO-5-(FORMYLAMINO)PYRIMIDIN-4-YL]AMINO}-2-HYDROXYCYCLOPENTYL]METHYL+DIHYDROGEN+PHOSPHATE'>FAX</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAX:[(1R,2S,4R)-4-{[6-AMINO-5-(FORMYLAMINO)PYRIMIDIN-4-YL]AMINO}-2-HYDROXYCYCLOPENTYL]METHYL+DIHYDROGEN+PHOSPHATE'>FAX</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">[[2xo7|2xo7]], [[2xy5|2xy5]], [[2xy6|2xy6]], [[2xy7|2xy7]], [[2y1i|2y1i]], [[2y1j|2y1j]], [[4b9l|4b9l]], [[4b9m|4b9m]], [[4b9s|4b9s]], [[4b9t|4b9t]], [[4b9u|4b9u]], [[4b9v|4b9v]]</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=4b9n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4b9n OCA], [https://pdbe.org/4b9n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4b9n RCSB], [https://www.ebi.ac.uk/pdbsum/4b9n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4b9n 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=4b9n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4b9n OCA], [http://pdbe.org/4b9n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4b9n RCSB], [http://www.ebi.ac.uk/pdbsum/4b9n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4b9n ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/E1C9K5_GEOSE E1C9K5_GEOSE] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[DNA polymerase|DNA polymerase]] | + | *[[DNA polymerase 3D structures|DNA polymerase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 12980]] | + | [[Category: Geobacillus stearothermophilus]] |
| - | [[Category: DNA-directed DNA polymerase]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Arnold, S]] | + | [[Category: Arnold S]] |
| - | [[Category: Carell, T]] | + | [[Category: Carell T]] |
| - | [[Category: Gehrke, T H]] | + | [[Category: Gehrke TH]] |
| - | [[Category: Lischke, U]] | + | [[Category: Lischke U]] |
| - | [[Category: Schneider, S]] | + | [[Category: Schneider S]] |
| - | [[Category: Dna damage]]
| + | |
| - | [[Category: Oxidative dna lesion]]
| + | |
| - | [[Category: Trans lesion synthesis]]
| + | |
| - | [[Category: Transferase-dna complex]]
| + | |
| Structural highlights
4b9n 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 2.2Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
E1C9K5_GEOSE
Publication Abstract from PubMed
8-Oxopurines (8-oxodG and 8-oxodA) and formamidopyrimidines (FaPydG and FaPydA) are major oxidative DNA lesions involved in cancer development and aging. Their mutagenicity is believed to result from a conformational shift of the N9-C1' glycosidic bonds from anti to syn, which allows the lesions to form noncanonical Hoogsteen-type base pairs with incoming triphosphates during DNA replication. Here we present biochemical data and what are to our knowledge the first crystal structures of carbocyclic FaPydA and FaPydG containing DNA in complex with a high-fidelity polymerase. Crystallographic snapshots show that the cFaPy lesions keep the anti geometry of the glycosidic bond during error-free and error-prone replication. The observed dG.dC-->dT.dA transversion mutations are the result of base shifting and tautomerization.
Unexpected non-Hoogsteen-based mutagenicity mechanism of FaPy-DNA lesions.,Gehrke TH, Lischke U, Gasteiger KL, Schneider S, Arnold S, Muller HC, Stephenson DS, Zipse H, Carell T Nat Chem Biol. 2013 May 19. doi: 10.1038/nchembio.1254. PMID:23685671[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Gehrke TH, Lischke U, Gasteiger KL, Schneider S, Arnold S, Muller HC, Stephenson DS, Zipse H, Carell T. Unexpected non-Hoogsteen-based mutagenicity mechanism of FaPy-DNA lesions. Nat Chem Biol. 2013 May 19. doi: 10.1038/nchembio.1254. PMID:23685671 doi:10.1038/nchembio.1254
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