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3px4

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Current revision (13:34, 1 March 2024) (edit) (undo)
 
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<StructureSection load='3px4' size='340' side='right'caption='[[3px4]], [[Resolution|resolution]] 1.58&Aring;' scene=''>
<StructureSection load='3px4' size='340' side='right'caption='[[3px4]], [[Resolution|resolution]] 1.58&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3px4]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_kaustophilus"_prickett_1928 "bacillus kaustophilus" prickett 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PX4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PX4 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3px4]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PX4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PX4 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DCT:2,3-DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.582&#8491;</td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DCT:2,3-DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3pv8|3pv8]], [[3px0|3px0]], [[3px6|3px6]]</div></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">polA, GK2730 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1462 "Bacillus kaustophilus" Prickett 1928])</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=3px4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3px4 OCA], [https://pdbe.org/3px4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3px4 RCSB], [https://www.ebi.ac.uk/pdbsum/3px4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3px4 ProSAT]</span></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=3px4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3px4 OCA], [https://pdbe.org/3px4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3px4 RCSB], [https://www.ebi.ac.uk/pdbsum/3px4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3px4 ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Q5KWC1_GEOKA Q5KWC1_GEOKA]
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Even though high-fidelity polymerases copy DNA with remarkable accuracy, some base-pair mismatches are incorporated at low frequency, leading to spontaneous mutagenesis. Using high-resolution X-ray crystallographic analysis of a DNA polymerase that catalyzes replication in crystals, we observe that a C*A mismatch can mimic the shape of cognate base pairs at the site of incorporation. This shape mimicry enables the mismatch to evade the error detection mechanisms of the polymerase, which would normally either prevent mismatch incorporation or promote its nucleolytic excision. Movement of a single proton on one of the mismatched bases alters the hydrogen-bonding pattern such that a base pair forms with an overall shape that is virtually indistinguishable from a canonical, Watson-Crick base pair in double-stranded DNA. These observations provide structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis, a long-standing concept that has been difficult to demonstrate directly.
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Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis.,Wang W, Hellinga HW, Beese LS Proc Natl Acad Sci U S A. 2011 Oct 25;108(43):17644-8. Epub 2011 Oct 17. PMID:22006298<ref>PMID:22006298</ref>
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==See Also==
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3px4" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bacillus kaustophilus prickett 1928]]
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[[Category: Geobacillus kaustophilus]]
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[[Category: DNA-directed DNA polymerase]]
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[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Beese, L S]]
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[[Category: Beese LS]]
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[[Category: Wang, W]]
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[[Category: Wang W]]
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[[Category: Closed conformation]]
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[[Category: Cytosine-adenine]]
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[[Category: Dna polymerase i]]
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[[Category: Protein-dna complex]]
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[[Category: Transferase-dna complex]]
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Current revision

Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddCTP-dA Mismatch (wobble) in Ajar Conformation

PDB ID 3px4

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