View source for 3qsb


==Structure of E. coli polIIIbeta with (Z)-5-(1-((4'-Fluorobiphenyl-4-yl)methoxyimino)butyl)-2,2-dimethyl-4,6-dioxocyclohexanecarbonitrile==
<StructureSection load='3qsb' size='340' side='right'caption='[[3qsb]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3qsb]] 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=3QSB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QSB FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=743:(1R,5R)-5-{(1Z)-N-[(4-FLUOROBIPHENYL-4-YL)METHOXY]BUTANIMIDOYL}-2,2-DIMETHYL-4,6-DIOXOCYCLOHEXANECARBONITRILE'>743</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3qsb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qsb OCA], [https://pdbe.org/3qsb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qsb RCSB], [https://www.ebi.ac.uk/pdbsum/3qsb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qsb ProSAT]</span></td></tr>
</table>
== Function ==
[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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== Publication Abstract from PubMed ==
The bacterial replisome is a target for development of new antibiotics to combat drug resistant strains. The beta&lt;sub&gt;2&lt;/sub&gt; sliding clamp is an essential component of the replicative machinery, providing a platform for recruitment and function of other replisomal components and ensuring polymerase processivity during DNA replication and repair. A single binding region of the clamp is utilized by its binding partners, which all contain conserved binding motifs. The C-terminal Leu and Phe residues of these motifs are integral to the binding interaction. We acquired three dimensional structural information on the binding site in beta&lt;sub&gt;2 &lt;/sub&gt; by study of binding of modified peptides. Development of a three dimensional pharmacophore based on the C-terminal dipeptide of the motif enabled identification of compounds that on further development inhibited alpha-beta&lt;sub&gt;2 &lt;/sub&gt; interaction at low muM concentrations. We report the crystal structure of the complex containing one of these inhibitors, a biphenyl oxime, bound to beta&lt;sub&gt;2&lt;/sub&gt;, as a starting point for further inhibitor design.

Binding Inhibitors of the Bacterial Sliding Clamp by Design.,Wijffels G, Johnson WM, Oakley AJ, Turner K, Epa VC, Briscoe SJ, Polley M, Liepa AJ, Hofmann A, Buchardt J, Christensen C, Prosselkov P, Dalrymple BP, Alewood PF, Jennings PA, Dixon NE, Winkler DA J Med Chem. 2011 May 23. PMID:21604761<ref>PMID:21604761</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 3qsb" style="background-color:#fffaf0;"></div>

==See Also==
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia coli K-12]]
[[Category: Large Structures]]
[[Category: Alewood PF]]
[[Category: Briscoe SJ]]
[[Category: Buchardt J]]
[[Category: Christensen C]]
[[Category: Dalrymple BP]]
[[Category: Dixon NE]]
[[Category: Epa VC]]
[[Category: Hofmann A]]
[[Category: Jennings PA]]
[[Category: Johnson WM]]
[[Category: Liepa AJ]]
[[Category: Oakley AJ]]
[[Category: Polley M]]
[[Category: Prosselkov P]]
[[Category: Turner K]]
[[Category: Wijffels G]]
[[Category: Winkler DA]]