4tr8: Difference between revisions
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==Crystal structure of DNA polymerase sliding clamp from Pseudomonas aeruginosa== | ==Crystal structure of DNA polymerase sliding clamp from Pseudomonas aeruginosa== | ||
<StructureSection load='4tr8' size='340' side='right' caption='[[4tr8]], [[Resolution|resolution]] 1.80Å' scene=''> | <StructureSection load='4tr8' size='340' side='right'caption='[[4tr8]], [[Resolution|resolution]] 1.80Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4tr8]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TR8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TR8 FirstGlance]. <br> | <table><tr><td colspan='2'>[[4tr8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_152504 Pseudomonas aeruginosa 152504]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TR8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TR8 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"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PA15_0320650 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=983919 Pseudomonas aeruginosa 152504])</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='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=4tr8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tr8 OCA], [http://pdbe.org/4tr8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4tr8 RCSB], [http://www.ebi.ac.uk/pdbsum/4tr8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4tr8 ProSAT]</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=4tr8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tr8 OCA], [http://pdbe.org/4tr8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4tr8 RCSB], [http://www.ebi.ac.uk/pdbsum/4tr8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4tr8 ProSAT]</span></td></tr> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: DNA-directed DNA polymerase]] | [[Category: DNA-directed DNA polymerase]] | ||
[[Category: Large Structures]] | |||
[[Category: Pseudomonas aeruginosa 152504]] | |||
[[Category: Burnouf, D]] | [[Category: Burnouf, D]] | ||
[[Category: Ennifar, E]] | [[Category: Ennifar, E]] | ||
Revision as of 17:24, 10 May 2019
Crystal structure of DNA polymerase sliding clamp from Pseudomonas aeruginosaCrystal structure of DNA polymerase sliding clamp from Pseudomonas aeruginosa
Structural highlights
Function[V4MZL6_PSEAI] 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 (By similarity).[PIRNR:PIRNR000804] Publication Abstract from PubMedBacterial 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. See AlsoReferences
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