4k3m

From Proteopedia

(Difference between revisions)

Revision as of 11:22, 25 December 2014

E.coli sliding clamp in complex with AcALDLF peptide

Structural highlights

4k3m is a 3 chain structure with sequence from Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
Related:	1mmi, 4k3k, 4k3l, 4k3o, 4k3p, 4k3q, 4k3r, 4k3s
Gene:	DnaN (ECOLI)
Activity:	DNA-directed DNA polymerase, with EC number 2.7.7.7
Resources:	FirstGlance, OCA, RCSB, PDBsum

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

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.

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^[1]

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

References

↑ Yin Z, Kelso MJ, Beck JL, Oakley AJ. Structural and Thermodynamic Dissection of Linear Motif Recognition by the E. coli Sliding Clamp. J Med Chem. 2013 Nov 14;56(21):8665-73. doi: 10.1021/jm401118f. Epub 2013 Oct 22. PMID:24090409 doi:http://dx.doi.org/10.1021/jm401118f

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/4k3m"

@@ Line 9: / Line 9: @@
 <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=4k3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k3m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4k3m RCSB], [http://www.ebi.ac.uk/pdbsum/4k3m PDBsum]</span></td></tr>
 </table>
+== Function ==
+[[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.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==

4k3m

From Proteopedia

Revision as of 11:22, 25 December 2014

E.coli sliding clamp in complex with AcALDLF peptide

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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