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3q4l

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Revision as of 07:41, 4 August 2016

Structure of a small peptide ligand bound to E.coli DNA sliding clamp

Structural highlights

3q4l is a 4 chain structure with sequence from Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:	, ,
Related:	1ok7, 3q4j, 3q4k, 3d1e, 3d1f, 3d1g
Gene:	dnaN, b3701, JW3678 (ECOLI)
Activity:	DNA-directed DNA polymerase, with EC number 2.7.7.7
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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.

Publication Abstract from PubMed

The multimeric DNA sliding clamps confer high processivity to replicative DNA polymerases and are also binding platforms for various enzymes involved in DNA metabolism. These enzymes interact with the clamp through a small peptide that binds into a hydrophobic pocket which is a potential target for the development of new antibacterial compounds. Starting from a generic heptapeptide, we used a structure-based strategy to improve the design of new peptide ligands. Chemical modifications at specific residues result in a dramatic increase of the interaction as measured by SPR and ITC. The affinity of our best hits was improved by 2 orders of magnitude as compared to the natural ligand, reaching 10(-8) M range. The molecular basis of the interactions was analyzed by solving the co-crystal structures of the most relevant peptides bound to the clamp and reveals how chemical modifications establish new contacts and contributes to an increased affinity of the ligand.

Structure-based design of short peptide ligands binding onto the E. coli processivity ring.,Wolff P, Olieric V, Briand JP, Chaloin O, Dejaegere A, Dumas P, Ennifar E, Guichard G, Wagner J, Burnouf DY J Med Chem. 2011 Jul 14;54(13):4627-37. doi: 10.1021/jm200311m. Epub 2011 Jun 9. PMID:21619076^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Wolff P, Olieric V, Briand JP, Chaloin O, Dejaegere A, Dumas P, Ennifar E, Guichard G, Wagner J, Burnouf DY. Structure-based design of short peptide ligands binding onto the E. coli processivity ring. J Med Chem. 2011 Jul 14;54(13):4627-37. doi: 10.1021/jm200311m. Epub 2011 Jun 9. PMID:21619076 doi:http://dx.doi.org/10.1021/jm200311m

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3q4l"

@@ Line 1: / Line 1: @@
 ==Structure of a small peptide ligand bound to E.coli DNA sliding clamp==
 <StructureSection load='3q4l' size='340' side='right' caption='[[3q4l]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
@@ Line 8: / Line 9: @@
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dnaN, b3701, JW3678 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3q4l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q4l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3q4l RCSB], [http://www.ebi.ac.uk/pdbsum/3q4l PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3q4l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q4l OCA], [http://pdbe.org/3q4l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3q4l RCSB], [http://www.ebi.ac.uk/pdbsum/3q4l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3q4l ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 20: / Line 21: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3q4l" style="background-color:#fffaf0;"></div>
 ==See Also==

3q4l

From Proteopedia

Revision as of 07:41, 4 August 2016

Structure of a small peptide ligand bound to E.coli DNA sliding clamp

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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