4b9v
From Proteopedia
(Difference between revisions)
| (5 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| - | {{STRUCTURE_4b9v| PDB=4b9v | SCENE= }} | ||
| - | ===Structure of the high fidelity DNA polymerase I with extending from an oxidative formamidopyrimidine-dG DNA lesion -dA basepair.=== | ||
| - | == | + | ==Structure of the high fidelity DNA polymerase I with extending from an oxidative formamidopyrimidine-dG DNA lesion -dA basepair.== |
| - | [[4b9v]] is a 3 chain structure with sequence from [ | + | <StructureSection load='4b9v' size='340' side='right'caption='[[4b9v]], [[Resolution|resolution]] 2.00Å' scene=''> |
| - | [[ | + | == Structural highlights == |
| + | <table><tr><td colspan='2'>[[4b9v]] 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=4B9V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4B9V FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FOX:((1R,2S,4R)-4-{[2-AMINO-5-(FORMYLAMINO)-6-OXO-3,6-DIHYDROPYRIMIDIN-4-YL]AMINO}-2-HYDROXYCYCLOPENTYL)METHYL+5-PHOSPHATE'>FOX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=4b9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4b9v OCA], [https://pdbe.org/4b9v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4b9v RCSB], [https://www.ebi.ac.uk/pdbsum/4b9v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4b9v ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/E1C9K5_GEOSE E1C9K5_GEOSE] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == 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<ref>PMID:23685671</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 4b9v" style="background-color:#fffaf0;"></div> | ||
| + | |||
| + | ==See Also== | ||
| + | *[[DNA polymerase 3D structures|DNA polymerase 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
[[Category: Geobacillus stearothermophilus]] | [[Category: Geobacillus stearothermophilus]] | ||
| - | [[Category: Arnold | + | [[Category: Large Structures]] |
| - | [[Category: Carell | + | [[Category: Arnold S]] |
| - | [[Category: Gehrke | + | [[Category: Carell T]] |
| - | [[Category: Lischke | + | [[Category: Gehrke TH]] |
| - | [[Category: Schneider | + | [[Category: Lischke U]] |
| - | + | [[Category: Schneider S]] | |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
Current revision
Structure of the high fidelity DNA polymerase I with extending from an oxidative formamidopyrimidine-dG DNA lesion -dA basepair.
| |||||||||||
