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4tr6

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Revision as of 10:51, 15 March 2023

Crystal structure of DNA polymerase sliding clamp from Bacillus subtilis

Structural highlights

4tr6 is a 2 chain structure with sequence from Bacillus subtilis subsp. subtilis str. 168. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DPO3B_BACSU 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

Bacterial sliding clamps are molecular hubs that interact with many proteins involved in DNA metabolism through their binding, via a conserved peptidic sequence, into a universally conserved pocket. This interacting pocket is acknowledged as a potential molecular target for the development of new antibiotics. We previously designed short peptides with an improved affinity for the Escherichia coli binding pocket. Here we show that these peptides differentially interact with other bacterial clamps, despite the fact that all pockets are structurally similar. Thermodynamic and modeling analyses of the interactions differentiate between two categories of clamps: group I clamps interacts efficiently with our designed peptides and assembles the Escherichia coli and related orthologs clamps, while group II poorly interact with the same peptides and includes Bacillus subtilis and other Gram+ clamps. These studies also suggest that the peptide binding process could occur via different mechanisms depending on which type of clamp it binds to.

Differential Modes of Peptide Binding onto Replicative Sliding Clamps from Various Bacterial Origins.,Wolff P, Amal I, Olieric V, Chaloin O, Gygli G, Ennifar E, Lorber B, Guichard G, Wagner JE, Dejaegere A, Burnouf DY J Med Chem. 2014 Aug 29. PMID:25170813^[1]

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

References

↑ Wolff P, Amal I, Olieric V, Chaloin O, Gygli G, Ennifar E, Lorber B, Guichard G, Wagner JE, Dejaegere A, Burnouf DY. Differential Modes of Peptide Binding onto Replicative Sliding Clamps from Various Bacterial Origins. J Med Chem. 2014 Aug 29. PMID:25170813 doi:http://dx.doi.org/10.1021/jm500467a

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/4tr6"

@@ Line 3: / Line 3: @@
 <StructureSection load='4tr6' size='340' side='right'caption='[[4tr6]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4tr6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TR6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TR6 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4tr6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TR6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4TR6 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>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dnaN, dnaG, BSU00020 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</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=4tr6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tr6 OCA], [https://pdbe.org/4tr6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4tr6 RCSB], [https://www.ebi.ac.uk/pdbsum/4tr6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4tr6 ProSAT]</span></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=4tr6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tr6 OCA], [http://pdbe.org/4tr6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4tr6 RCSB], [http://www.ebi.ac.uk/pdbsum/4tr6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4tr6 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DPO3B_BACSU DPO3B_BACSU]] 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.
+[https://www.uniprot.org/uniprot/DPO3B_BACSU DPO3B_BACSU] 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 ==
@@ Line 22: / Line 20: @@
 ==See Also==
-*[[DNA polymerase|DNA polymerase]]
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacsu]]
+[[Category: Bacillus subtilis subsp. subtilis str. 168]]
-[[Category: DNA-directed DNA polymerase]]
 [[Category: Large Structures]]
-[[Category: Burnouf, D]]
+[[Category: Burnouf D]]
-[[Category: Ennifar, E]]
+[[Category: Ennifar E]]
-[[Category: Olieric, V]]
+[[Category: Olieric V]]
-[[Category: Wolff, P]]
+[[Category: Wolff P]]
-[[Category: Dna binding protein]]
-[[Category: Dna polymerase]]
-[[Category: Processivity]]
-[[Category: Sliding clamp]]

4tr6

From Proteopedia

Revision as of 10:51, 15 March 2023

Crystal structure of DNA polymerase sliding clamp from Bacillus subtilis

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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