4k3m

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{{STRUCTURE_4k3m| PDB=4k3m | SCENE= }}
 
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===E.coli sliding clamp in complex with AcALDLF peptide===
 
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{{ABSTRACT_PUBMED_24090409}}
 
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==Function==
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==E.coli sliding clamp in complex with AcALDLF peptide==
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[[http://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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<StructureSection load='4k3m' size='340' side='right'caption='[[4k3m]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[4k3m]] is a 3 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=4K3M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4K3M FirstGlance]. <br>
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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]] 1.85&#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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
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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=4k3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k3m OCA], [https://pdbe.org/4k3m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4k3m RCSB], [https://www.ebi.ac.uk/pdbsum/4k3m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4k3m 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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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Protein-protein interactions based on linear motif (LM) recognition play roles in many cell regulatory processes. The E. coli sliding clamp is a protein mediator of replisome formation, which uses a common surface pocket composed of two subsites (I and II) to interact with LMs in multiple binding partners. A structural and thermodynamic dissection of sliding clamp-LM recognition has been performed, providing support for a sequential binding model. According to the model, a hydrophobic C-terminal LM dipeptide submotif acts as an anchor to establish initial contacts within subsite I, and this is followed by formation of a stabilizing hydrogen-bonding network between the flanking LM residues and subsite II. Differential solvation/desolvation during positioning of the submotifs is proposed as a driver for the sequential binding. Our model provides general insights into linear motif recognition and should guide the design of small-molecule inhibitors of the E. coli sliding clamp, an emerging antibacterial target.
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==About this Structure==
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Structural and Thermodynamic Dissection of Linear Motif Recognition by the E. coli Sliding Clamp.,Yin Z, Kelso MJ, Beck JL, Oakley AJ J Med Chem. 2013 Nov 14;56(21):8665-73. doi: 10.1021/jm401118f. Epub 2013 Oct 22. PMID:24090409<ref>PMID:24090409</ref>
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[[4k3m]] is a 3 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=4K3M OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<ref group="xtra">PMID:024090409</ref><references group="xtra"/><references/>
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</div>
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[[Category: DNA-directed DNA polymerase]]
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<div class="pdbe-citations 4k3m" style="background-color:#fffaf0;"></div>
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[[Category: Ecoli]]
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[[Category: Oakley, A J.]]
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==See Also==
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[[Category: Yin, Z.]]
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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[[Category: E. coli sliding clamp]]
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== References ==
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[[Category: Transferase]]
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Escherichia coli K-12]]
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[[Category: Large Structures]]
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[[Category: Oakley AJ]]
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[[Category: Yin Z]]

Current revision

E.coli sliding clamp in complex with AcALDLF peptide

PDB ID 4k3m

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