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3tfr

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==Ternary complex structure of DNA polymerase beta with a gapped DNA substrate and a, b dAMP(CF2)PP in the active site==
==Ternary complex structure of DNA polymerase beta with a gapped DNA substrate and a, b dAMP(CF2)PP in the active site==
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<StructureSection load='3tfr' size='340' side='right' caption='[[3tfr]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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<StructureSection load='3tfr' size='340' side='right'caption='[[3tfr]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3tfr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TFR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TFR FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3tfr]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TFR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TFR 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=F3A:2-DEOXY-5-O-[(S)-{DIFLUORO[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]METHYL}(HYDROXY)PHOSPHORYL]ADENOSINE'>F3A</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3tfs|3tfs]]</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F3A:2-DEOXY-5-O-[(S)-{DIFLUORO[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]METHYL}(HYDROXY)PHOSPHORYL]ADENOSINE'>F3A</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">POLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=3tfr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tfr OCA], [https://pdbe.org/3tfr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tfr RCSB], [https://www.ebi.ac.uk/pdbsum/3tfr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tfr ProSAT]</span></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=3tfr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tfr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tfr RCSB], [http://www.ebi.ac.uk/pdbsum/3tfr PDBsum]</span></td></tr>
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</table>
</table>
== Function ==
== 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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[https://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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The influence of water: Crystallization of (R/S)-alpha,beta-CHF-dATP with the preorganized pol beta-DNA complex shows that (S)-alpha,beta-CHF-dATP is preferentially bound to the active site with the CF fluorine proximal to a structural water bound to Asp276.
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Stereospecific Formation of a Ternary Complex of (S)-alpha,beta-Fluoromethylene-dATP with DNA Pol beta.,Chamberlain BT, Batra VK, Beard WA, Kadina AP, Shock DD, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH Chembiochem. 2012 Mar 5;13(4):528-30. doi: 10.1002/cbic.201100738. Epub 2012 Feb , 7. PMID:22315190<ref>PMID:22315190</ref>
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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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==See Also==
==See Also==
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*[[DNA polymerase|DNA polymerase]]
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Batra, V K]]
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[[Category: Large Structures]]
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[[Category: Beard, W A]]
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[[Category: Batra VK]]
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[[Category: Chamberlain, B T]]
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[[Category: Beard WA]]
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[[Category: Goodman, M F]]
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[[Category: Chamberlain BT]]
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[[Category: Kadina, A P]]
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[[Category: Goodman MF]]
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[[Category: Kashemirov, B A]]
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[[Category: Kadina AP]]
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[[Category: McKenna, C E]]
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[[Category: Kashemirov BA]]
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[[Category: Shock, D D]]
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[[Category: McKenna CE]]
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[[Category: Wilson, S H]]
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[[Category: Shock DD]]
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[[Category: Dna polymerase]]
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[[Category: Wilson SH]]
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[[Category: Stereoselectivity]]
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[[Category: Transferase-dna complex]]
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Current revision

Ternary complex structure of DNA polymerase beta with a gapped DNA substrate and a, b dAMP(CF2)PP in the active site

PDB ID 3tfr

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