2jgu

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[[Image:2jgu.png|left|200px]]
 
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{{STRUCTURE_2jgu| PDB=2jgu | SCENE= }}
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==crystal structure of DNA-directed DNA polymerase==
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<StructureSection load='2jgu' size='340' side='right'caption='[[2jgu]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2jgu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JGU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JGU FirstGlance]. <br>
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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]] 2.6&#8491;</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=MN:MANGANESE+(II)+ION'>MN</scene></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=2jgu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jgu OCA], [https://pdbe.org/2jgu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jgu RCSB], [https://www.ebi.ac.uk/pdbsum/2jgu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jgu ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DPOL_PYRFU DPOL_PYRFU] In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' exonuclease activity.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jg/2jgu_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2jgu ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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We have determined a 2.6A resolution crystal structure of Pfu DNA polymerase, the most commonly used high fidelity PCR enzyme, from Pyrococcus furiosus. Although the structures of Pfu and KOD1 are highly similar, the structure of Pfu elucidates the electron density of the interface between the exonuclease and thumb domains, which has not been previously observed in the KOD1 structure. The interaction of these two domains is known to coordinate the proofreading and polymerization activity of DNA polymerases, especially via H147 that is present within the loop (residues 144-158) of the exonuclease domain. In our structure of Pfu, however, E148 rather than H147 is located at better position to interact with the thumb domain. In addition, the structural analysis of Pfu and KOD1 shows that both the Y-GG/A and beta-hairpin motifs of Pfu are found to differ with that of KOD1, and may explain differences in processivity. This information enables us to better understand the mechanisms of polymerization and proofreading of DNA polymerases.
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===CRYSTAL STRUCTURE OF DNA-DIRECTED DNA POLYMERASE===
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Crystal structure of Pfu, the high fidelity DNA polymerase from Pyrococcus furiosus.,Kim SW, Kim DU, Kim JK, Kang LW, Cho HS Int J Biol Macromol. 2008 May 1;42(4):356-61. Epub 2008 Feb 12. PMID:18355915<ref>PMID:18355915</ref>
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{{ABSTRACT_PUBMED_18355915}}
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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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==About this Structure==
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<div class="pdbe-citations 2jgu" style="background-color:#fffaf0;"></div>
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[[2jgu]] is a 1 chain structure of [[DNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JGU OCA].
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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]]
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== References ==
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==Reference==
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<references/>
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<ref group="xtra">PMID:018355915</ref><references group="xtra"/>
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__TOC__
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[[Category: DNA-directed DNA polymerase]]
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Pyrococcus furiosus]]
[[Category: Pyrococcus furiosus]]
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[[Category: Cho, H S.]]
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[[Category: Cho HS]]
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[[Category: Kim, D U.]]
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[[Category: Kim DU]]
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[[Category: Dna replication]]
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[[Category: Dna-binding]]
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[[Category: Dna-directed dna polymerase]]
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[[Category: Endonuclease]]
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[[Category: Hydrolase]]
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[[Category: Nuclease]]
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[[Category: Nucleotidyltransferase]]
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[[Category: Pfu]]
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[[Category: Transferase]]
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Current revision

crystal structure of DNA-directed DNA polymerase

PDB ID 2jgu

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