3q4l: Difference between revisions

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[[Image:3q4l.png|left|200px]]
==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=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3q4l]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q4L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3Q4L FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=ALC:2-AMINO-3-CYCLOHEXYL-PROPIONIC+ACID'>ALC</scene>, <scene name='pdbligand=ZCL:3,4-DICHLORO-L-PHENYLALANINE'>ZCL</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ok7|1ok7]], [[3q4j|3q4j]], [[3q4k|3q4k]], [[3d1e|3d1e]], [[3d1f|3d1f]], [[3d1g|3d1g]]</td></tr>
<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>
</table>
<div style="background-color:#fffaf0;">
== 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_3q4l|  PDB=3q4l  |  SCENE=  }}
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<ref>PMID:21619076</ref>


===Structure of a small peptide ligand bound to E.coli DNA sliding clamp===
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
 
==About this Structure==
[[3q4l]] is a 4 chain structure with sequence 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=3Q4L OCA].


==See Also==
==See Also==
*[[DNA polymerase|DNA polymerase]]
*[[DNA polymerase|DNA polymerase]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: DNA-directed DNA polymerase]]
[[Category: DNA-directed DNA polymerase]]
[[Category: Escherichia coli]]
[[Category: Ecoli]]
[[Category: Briand, J P.]]
[[Category: Briand, J P]]
[[Category: Burnouf, D.]]
[[Category: Burnouf, D]]
[[Category: Chaloin, O.]]
[[Category: Chaloin, O]]
[[Category: Dejaegere, A.]]
[[Category: Dejaegere, A]]
[[Category: Dumas, P.]]
[[Category: Dumas, P]]
[[Category: Ennifar, E.]]
[[Category: Ennifar, E]]
[[Category: Guichard, G.]]
[[Category: Guichard, G]]
[[Category: Olieric, V.]]
[[Category: Olieric, V]]
[[Category: Wagner, J.]]
[[Category: Wagner, J]]
[[Category: Wolff, P.]]
[[Category: Wolff, P]]
[[Category: Dna polymerase]]
[[Category: Dna polymerase]]
[[Category: Dna replication]]
[[Category: Dna replication]]

Revision as of 14:17, 9 December 2014

Structure of a small peptide ligand bound to E.coli DNA sliding clampStructure 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:, ,
Gene:dnaN, b3701, JW3678 (ECOLI)
Activity:DNA-directed DNA polymerase, with EC number 2.7.7.7
Resources:FirstGlance, OCA, RCSB, PDBsum

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.

See Also

References

  1. ↑ 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

3q4l, resolution 1.95Å

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