3bep

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[[Image:3bep.jpg|left|200px]]
 
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{{Structure
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==Structure of a sliding clamp on DNA==
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|PDB= 3bep |SIZE=350|CAPTION= <scene name='initialview01'>3bep</scene>, resolution 1.920&Aring;
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<StructureSection load='3bep' size='340' side='right'caption='[[3bep]], [[Resolution|resolution]] 1.92&Aring;' scene=''>
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|SITE= <scene name='pdbsite=AC1:5cy+Binding+Site+For+Residue+C+111'>AC1</scene>
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=5CY:N,N&#39;-(DIPROPYL)-TETRAMETHYLINDODICARBOCYANINE'>5CY</scene>, <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>
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<table><tr><td colspan='2'>[[3bep]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BEP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BEP FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span>
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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]] 1.92&#8491;</td></tr>
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|GENE= dnaN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CY:1-(3-HYDROXYPROPYL)-2-{(1E,3E,5E)-5-[1-(3-HYDROXYPROPYL)-3,3-DIMETHYL-1,3-DIHYDRO-2H-INDOL-2-YLIDENE]PENTA-1,3-DIEN-1-YL}-3,3-DIMETHYL-3H-INDOLIUM'>5CY</scene></td></tr>
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|DOMAIN=
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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=3bep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bep OCA], [https://pdbe.org/3bep PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bep RCSB], [https://www.ebi.ac.uk/pdbsum/3bep PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bep ProSAT]</span></td></tr>
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|RELATEDENTRY=[[2pol|2POL]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3bep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bep OCA], [http://www.ebi.ac.uk/pdbsum/3bep PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3bep RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/DPO3B_ECOLI DPO3B_ECOLI] DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The beta chain is required for initiation of replication once it is clamped onto DNA, it slides freely (bidirectional and ATP-independent) along duplex DNA.
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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/be/3bep_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=3bep 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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The structure of the E. coli beta clamp polymerase processivity factor has been solved in complex with primed DNA. Interestingly, the clamp directly binds the DNA duplex and also forms a crystal contact with the ssDNA template strand, which binds into the protein-binding pocket of the clamp. We demonstrate that these clamp-DNA interactions function in clamp loading, perhaps by inducing the ring to close around DNA. Clamp binding to template ssDNA may also serve to hold the clamp at a primed site after loading or during switching of multiple factors on the clamp. Remarkably, the DNA is highly tilted as it passes through the beta ring. The pronounced 22 degrees angle of DNA through beta may enable DNA to switch between multiple factors bound to a single clamp simply by alternating from one protomer of the ring to the other.
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'''Structure of a sliding clamp on DNA'''
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Structure of a sliding clamp on DNA.,Georgescu RE, Kim SS, Yurieva O, Kuriyan J, Kong XP, O'Donnell M Cell. 2008 Jan 11;132(1):43-54. PMID:18191219<ref>PMID:18191219</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 3bep" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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The structure of the E. coli beta clamp polymerase processivity factor has been solved in complex with primed DNA. Interestingly, the clamp directly binds the DNA duplex and also forms a crystal contact with the ssDNA template strand, which binds into the protein-binding pocket of the clamp. We demonstrate that these clamp-DNA interactions function in clamp loading, perhaps by inducing the ring to close around DNA. Clamp binding to template ssDNA may also serve to hold the clamp at a primed site after loading or during switching of multiple factors on the clamp. Remarkably, the DNA is highly tilted as it passes through the beta ring. The pronounced 22 degrees angle of DNA through beta may enable DNA to switch between multiple factors bound to a single clamp simply by alternating from one protomer of the ring to the other.
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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3BEP is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BEP OCA].
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__TOC__
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</StructureSection>
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==Reference==
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Structure of a sliding clamp on DNA., Georgescu RE, Kim SS, Yurieva O, Kuriyan J, Kong XP, O'Donnell M, Cell. 2008 Jan 11;132(1):43-54. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18191219 18191219]
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[[Category: DNA-directed DNA polymerase]]
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[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Protein complex]]
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[[Category: Large Structures]]
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[[Category: Donnell, M O.]]
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[[Category: Georgescu RE]]
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[[Category: Georgescu, R E.]]
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[[Category: Kim SS]]
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[[Category: Kim, S S.]]
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[[Category: Kong X-P]]
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[[Category: Kong, X P.]]
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[[Category: Kuriyan J]]
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[[Category: Kuriyan, J.]]
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[[Category: O'Donnell M]]
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[[Category: Yurieva, O.]]
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[[Category: Yurieva O]]
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[[Category: beta subunit]]
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[[Category: dna complex]]
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[[Category: e. coli polymerase iii]]
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[[Category: sliding clamp]]
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[[Category: transcription/dna complex]]
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[[Category: transferase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:25:34 2008''
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Current revision

Structure of a sliding clamp on DNA

PDB ID 3bep

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