3d1g

From Proteopedia

(Difference between revisions)

Revision as of 19:13, 24 January 2018

Structure of a small molecule inhibitor bound to a DNA sliding clamp

Structural highlights

3d1g is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	2pol, 3bep, 3d1e, 3d1f
Gene:	dnaN (Escherichia coli)
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.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

DNA polymerases attach to the DNA sliding clamp through a common overlapping binding site. We identify a small-molecule compound that binds the protein-binding site in the Escherichia coli beta-clamp and differentially affects the activity of DNA polymerases II, III, and IV. To understand the molecular basis of this discrimination, the cocrystal structure of the chemical inhibitor is solved in complex with beta and is compared with the structures of Pol II, Pol III, and Pol IV peptides bound to beta. The analysis reveals that the small molecule localizes in a region of the clamp to which the DNA polymerases attach in different ways. The results suggest that the small molecule may be useful in the future to probe polymerase function with beta, and that the beta-clamp may represent an antibiotic target.

Structure of a small-molecule inhibitor of a DNA polymerase sliding clamp.,Georgescu RE, Yurieva O, Kim SS, Kuriyan J, Kong XP, O'Donnell M Proc Natl Acad Sci U S A. 2008 Aug 12;105(32):11116-21. Epub 2008 Aug 4. PMID:18678908^[1]

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

References

↑ Georgescu RE, Yurieva O, Kim SS, Kuriyan J, Kong XP, O'Donnell M. Structure of a small-molecule inhibitor of a DNA polymerase sliding clamp. Proc Natl Acad Sci U S A. 2008 Aug 12;105(32):11116-21. Epub 2008 Aug 4. PMID:18678908

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3d1g"

@@ Line 16: / Line 16: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d1/3d1g_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d1/3d1g_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 39: / Line 39: @@
 [[Category: Donnell, M O]]
 [[Category: Georgescu, R E]]
-[[Category: Kong, X-P]]
+[[Category: Kong, X P]]
 [[Category: Kuriyan, J]]
 [[Category: Seung-Sup, K]]

3d1g

From Proteopedia

Revision as of 19:13, 24 January 2018

Structure of a small molecule inhibitor bound to a DNA sliding clamp

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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