View source for 1ok7


==A Conserved protein binding-site on Bacterial Sliding Clamps==
<StructureSection load='1ok7' size='340' side='right'caption='[[1ok7]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1ok7]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OK7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OK7 FirstGlance]. <br>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1jqj|1jqj]], [[1jql|1jql]], [[2pol|2pol]]</div></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=1ok7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ok7 OCA], [https://pdbe.org/1ok7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ok7 RCSB], [https://www.ebi.ac.uk/pdbsum/1ok7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ok7 ProSAT]</span></td></tr>
</table>
== Function ==
[[https://www.uniprot.org/uniprot/DPO4_ECOLI DPO4_ECOLI]] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. Overexpression of polIV results in increased frameshift mutagenesis. It is required for stationary-phase adaptive mutation, which provides the bacterium with flexibility in dealing with environmental stress, enhancing long-term survival and evolutionary fitness. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII.<ref>PMID:9391106</ref> <ref>PMID:11080171</ref> <ref>PMID:11463382</ref> <ref>PMID:11751576</ref> <ref>PMID:12060704</ref>  
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ok/1ok7_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=1ok7 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Most DNA polymerases interact with their cognate processive replication factor through a small peptide, this interaction being absolutely required for their function in vivo. We have solved the crystal structure of a complex between the beta sliding clamp of Escherichia coli and the 16 residue C-terminal peptide of Pol IV (P16). The seven C-terminal residues bind to a pocket located at the surface of one beta monomer. This region was previously identified as the binding site of another beta clamp binding protein, the delta subunit of the gamma complex. We show that peptide P16 competitively prevents beta-clamp-mediated stimulation of both Pol IV and alpha subunit DNA polymerase activities, suggesting that the site of interaction of the alpha subunit with beta is identical with, or overlaps that of Pol IV. This common binding site for delta, Pol IV and alpha subunit is shown to be formed by residues that are highly conserved among many bacterial beta homologs, thus defining an evolutionarily conserved hydrophobic crevice for sliding clamp ligands and a new target for antibiotic drug design.

Structural and biochemical analysis of sliding clamp/ligand interactions suggest a competition between replicative and translesion DNA polymerases.,Burnouf DY, Olieric V, Wagner J, Fujii S, Reinbolt J, Fuchs RP, Dumas P J Mol Biol. 2004 Jan 30;335(5):1187-97. PMID:14729336<ref>PMID:14729336</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1ok7" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Bacillus coli migula 1895]]
[[Category: DNA-directed DNA polymerase]]
[[Category: Large Structures]]
[[Category: Burnouf, D Y]]
[[Category: Dumas, P]]
[[Category: Fuchs, R P.P]]
[[Category: Fujii, S]]
[[Category: Olieric, V]]
[[Category: Reinbolt, J]]
[[Category: Wagner, J]]
[[Category: Dna polymerase iv]]
[[Category: Dna replication]]
[[Category: Dna-directed dna polymerase]]
[[Category: Peptide inhibition]]
[[Category: Sliding clamp]]
[[Category: Transferase]]
[[Category: Translesion synthesis]]