3d1g

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[[Image:3d1g.png|left|200px]]
 
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==Structure of a small molecule inhibitor bound to a DNA sliding clamp==
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The line below this paragraph, containing "STRUCTURE_3d1g", creates the "Structure Box" on the page.
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<StructureSection load='3d1g' size='340' side='right'caption='[[3d1g]], [[Resolution|resolution]] 1.64&Aring;' 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'>[[3d1g]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D1G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D1G FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 1.64&#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=322:[(5R)-5-(2,3-DIBROMO-5-ETHOXY-4-HYDROXYBENZYL)-4-OXO-2-THIOXO-1,3-THIAZOLIDIN-3-YL]ACETIC+ACID'>322</scene></td></tr>
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{{STRUCTURE_3d1g| PDB=3d1g | 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=3d1g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d1g OCA], [https://pdbe.org/3d1g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d1g RCSB], [https://www.ebi.ac.uk/pdbsum/3d1g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d1g ProSAT]</span></td></tr>
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</table>
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== Function ==
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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/d1/3d1g_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=3d1g 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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DNA polymerases attach to the DNA sliding clamp through a common overlapping binding site. We identify a small-molecule compound that binds the protein-binding site in the Escherichia coli beta-clamp and differentially affects the activity of DNA polymerases II, III, and IV. To understand the molecular basis of this discrimination, the cocrystal structure of the chemical inhibitor is solved in complex with beta and is compared with the structures of Pol II, Pol III, and Pol IV peptides bound to beta. The analysis reveals that the small molecule localizes in a region of the clamp to which the DNA polymerases attach in different ways. The results suggest that the small molecule may be useful in the future to probe polymerase function with beta, and that the beta-clamp may represent an antibiotic target.
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===Structure of a small molecule inhibitor bound to a DNA sliding clamp===
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Structure of a small-molecule inhibitor of a DNA polymerase sliding clamp.,Georgescu RE, Yurieva O, Kim SS, Kuriyan J, Kong XP, O'Donnell M Proc Natl Acad Sci U S A. 2008 Aug 12;105(32):11116-21. Epub 2008 Aug 4. PMID:18678908<ref>PMID:18678908</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 3d1g" style="background-color:#fffaf0;"></div>
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==About this Structure==
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==See Also==
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3D1G is a 2 chains 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=3D1G OCA].
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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[[Category: DNA-directed DNA polymerase]]
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== References ==
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[[Category: Escherichia coli]]
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<references/>
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[[Category: Donnell, M O.]]
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__TOC__
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[[Category: Georgescu, R E.]]
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</StructureSection>
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[[Category: Kong, X-P.]]
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[[Category: Escherichia coli K-12]]
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[[Category: Kuriyan, J.]]
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[[Category: Large Structures]]
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[[Category: Seung-Sup, K.]]
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[[Category: Georgescu RE]]
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[[Category: Yurieva, O.]]
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[[Category: Kong X-P]]
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[[Category: Antibiotic target]]
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[[Category: Kuriyan J]]
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[[Category: Chemical probe]]
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[[Category: O'Donnell M]]
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[[Category: Dna polymerase]]
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[[Category: Seung-Sup K]]
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[[Category: Dna replication]]
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[[Category: Yurieva O]]
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[[Category: Dna sliding clamp]]
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[[Category: Rational drug design]]
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[[Category: Transcription]]
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[[Category: Transferase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 14 12:46:13 2009''
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Current revision

Structure of a small molecule inhibitor bound to a DNA sliding clamp

PDB ID 3d1g

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