2xy8

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[[Image:2xy8.jpg|left|200px]]
 
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==Paramagnetic-based NMR structure of the complex between the N- terminal epsilon domain and the theta domain of the DNA polymerase III==
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The line below this paragraph, containing "STRUCTURE_2xy8", creates the "Structure Box" on the page.
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<StructureSection load='2xy8' size='340' side='right'caption='[[2xy8]]' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2xy8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XY8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XY8 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">Solution NMR</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=CA:CALCIUM+ION'>CA</scene></td></tr>
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{{STRUCTURE_2xy8| PDB=2xy8 | SCENE= }}
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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=2xy8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xy8 OCA], [https://pdbe.org/2xy8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xy8 RCSB], [https://www.ebi.ac.uk/pdbsum/2xy8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xy8 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DPO3E_ECOLI DPO3E_ECOLI] DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. The epsilon subunit contain the editing function and is a proofreading 3'-5' exonuclease.
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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In order to enhance the structure determination process of macromolecular assemblies by NMR, we have implemented long-range pseudocontact shift (PCS) restraints into the data-driven protein docking package HADDOCK. We demonstrate the efficiency of the method on a synthetic, yet realistic case based on the lanthanide-labeled N-terminal epsilon domain of the E. coli DNA polymerase III (epsilon186) in complex with the HOT domain. Docking from the bound form of the two partners is swiftly executed (interface RMSDs &lt; 1 A) even with addition of very large amount of noise, while the conformational changes of the free form still present some challenges (interface RMSDs in a 3.1-3.9 A range for the ten lowest energy complexes). Finally, using exclusively PCS as experimental information, we determine the structure of epsilon186 in complex with the HOT-homologue theta subunit of the E. coli DNA polymerase III.
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===PARAMAGNETIC-BASED NMR STRUCTURE OF THE COMPLEX BETWEEN THE N-TERMINAL EPSILON DOMAIN AND THE THETA DOMAIN OF THE DNA POLYMERASE III===
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Protein-protein HADDocking using exclusively pseudocontact shifts.,Schmitz C, Bonvin AM J Biomol NMR. 2011 May 29. PMID:21626213<ref>PMID:21626213</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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<div class="pdbe-citations 2xy8" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_21626213}}, adds the Publication Abstract to the page
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 21626213 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_21626213}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[2xy8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XY8 OCA].
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==Reference==
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<ref group="xtra">PMID:021626213</ref><ref group="xtra">PMID:018574699</ref><ref group="xtra">PMID:016536542</ref><ref group="xtra">PMID:017803234</ref><references group="xtra"/>
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[[Category: DNA-directed DNA polymerase]]
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[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Bonvin, A M.J J.]]
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[[Category: Large Structures]]
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[[Category: Schmitz, C.]]
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[[Category: Bonvin AMJJ]]
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[[Category: Docking]]
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[[Category: Schmitz C]]
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[[Category: Experimental restraint]]
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[[Category: Haddock program]]
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[[Category: Transferase]]
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Current revision

Paramagnetic-based NMR structure of the complex between the N- terminal epsilon domain and the theta domain of the DNA polymerase III

PDB ID 2xy8

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