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5j2k

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'''Unreleased structure'''
 
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The entry 5j2k is ON HOLD until Paper Publication
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==Ternary complex crystal structure of DNA polymerase Beta with T:T mismatch at the primer terminus==
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<StructureSection load='5j2k' size='340' side='right' caption='[[5j2k]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[5j2k]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J2K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J2K FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DUP:2-DEOXYURIDINE+5-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5j0o|5j0o]], [[5j0p|5j0p]], [[5j0q|5j0q]], [[5j0r|5j0r]], [[5j0s|5j0s]], [[5j0t|5j0t]], [[5j0u|5j0u]], [[5j0v|5j0v]], [[5j0w|5j0w]], [[5j0x|5j0x]], [[5j0y|5j0y]], [[5j29|5j29]], [[5j2a|5j2a]], [[5j2b|5j2b]], [[5j2c|5j2c]], [[5j2d|5j2d]], [[5j2e|5j2e]], [[5j2f|5j2f]], [[5j2g|5j2g]], [[5j2h|5j2h]], [[5j2i|5j2i]], [[5j2j|5j2j]]</td></tr>
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<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=5j2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j2k OCA], [http://pdbe.org/5j2k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j2k RCSB], [http://www.ebi.ac.uk/pdbsum/5j2k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j2k ProSAT]</span></td></tr>
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</table>
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== Function ==
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[[http://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN]] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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High-fidelity DNA synthesis requires that polymerases display a strong preference for right nucleotide insertion. When the wrong nucleotide is inserted, the polymerase deters extension from the mismatched DNA terminus. Twenty-three crystallographic structures of DNA polymerase beta with terminal template-primer mismatches were determined as binary DNA and ternary pre-catalytic substrate complexes. These structures indicate that the mismatched termini adopt various distorted conformations that attempt to satisfy stacking and hydrogen-bonding interactions. The binary complex structures indicate an induced strain in the mismatched template nucleotide. Addition of a non-hydrolyzable incoming nucleotide stabilizes the templating nucleotide with concomitant strain in the primer terminus. Several dead-end ternary complex structures suggest that DNA synthesis might occur as the enzyme transitions from an open to a closed complex. The structures are consistent with an induced-fit mechanism where a mismatched terminus is misaligned relative to the correct incoming nucleotide to deter or delay further DNA synthesis.
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Authors: Batra, V.K., Wilson, S.H.
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Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism.,Batra VK, Beard WA, Pedersen LC, Wilson SH Structure. 2016 Sep 13. pii: S0969-2126(16)30238-6. doi:, 10.1016/j.str.2016.08.006. PMID:27642161<ref>PMID:27642161</ref>
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Description: Ternary complex crystal structure of DNA polymerase Beta with T:T mismatch at the primer terminus
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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[[Category: Unreleased Structures]]
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</div>
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[[Category: Wilson, S.H]]
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<div class="pdbe-citations 5j2k" style="background-color:#fffaf0;"></div>
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[[Category: Batra, V.K]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Batra, V K]]
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[[Category: Wilson, S H]]
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[[Category: Dna polymerase beta]]
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[[Category: Mismatch extension]]
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[[Category: Ternary complex]]
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[[Category: Transferase-dna complex]]

Revision as of 18:31, 26 October 2016

Ternary complex crystal structure of DNA polymerase Beta with T:T mismatch at the primer terminus

5j2k, resolution 2.10Å

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