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| | <StructureSection load='6fvm' size='340' side='right'caption='[[6fvm]], [[Resolution|resolution]] 1.63Å' scene=''> | | <StructureSection load='6fvm' size='340' side='right'caption='[[6fvm]], [[Resolution|resolution]] 1.63Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6fvm]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FVM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6FVM FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6fvm]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 Escherichia coli O157:H7] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FVM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6FVM FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.631Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=ALC:2-AMINO-3-CYCLOHEXYL-PROPIONIC+ACID'>ALC</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=ALC:2-AMINO-3-CYCLOHEXYL-PROPIONIC+ACID'>ALC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=6fvm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fvm OCA], [http://pdbe.org/6fvm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6fvm RCSB], [http://www.ebi.ac.uk/pdbsum/6fvm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6fvm ProSAT]</span></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=6fvm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fvm OCA], [https://pdbe.org/6fvm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6fvm RCSB], [https://www.ebi.ac.uk/pdbsum/6fvm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6fvm ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DPO3B_ECO57 DPO3B_ECO57]] Confers DNA tethering and processivity to DNA polymerases and other proteins. Acts as a clamp, forming a ring around DNA (a reaction catalyzed by the clamp-loading complex) which diffuses in an ATP-independent manner freely and bidirectionally along dsDNA. Initially characterized for its ability to contact the catalytic subunit of DNA polymerase III (Pol III), a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria; Pol III exhibits 3'-5' exonuclease proofreading activity. The beta chain is required for initiation of replication as well as for processivity of DNA replication.[UniProtKB:P0A988] | + | [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. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6fvm" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6fvm" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[DNA polymerase 3D structures|DNA polymerase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Escherichia coli O157:H7]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Andre, C]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Burnouf, D]] | + | [[Category: Andre C]] |
| - | [[Category: Guichard, G]] | + | [[Category: Burnouf D]] |
| - | [[Category: Martiel, I]] | + | [[Category: Guichard G]] |
| - | [[Category: Olieric, V]] | + | [[Category: Martiel I]] |
| - | [[Category: Dna binding protein]]
| + | [[Category: Olieric V]] |
| - | [[Category: Dna sliding clamp]]
| + | |
| Structural highlights
6fvm is a 4 chain structure with sequence from Escherichia coli O157:H7 and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.631Å |
| Ligands: | , , , , |
| 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.
Publication Abstract from PubMed
Bacterial sliding clamps control the access of DNA polymerases to the replication fork and are appealing targets for antibacterial drug development. It is therefore essential to decipher the polymerase-clamp binding mode across various bacterial species. Here, two residues of the E. coli clamp binding pocket, (Ec)S346 and (Ec)M362, and their cognate residues in M. tuberculosis and B. subtilis clamps, were mutated. The effects of these mutations on the interaction of a model peptide with these variant clamps were evaluated by thermodynamic, molecular dynamics, X-rays crystallography, and biochemical analyses. (Ec)M362 and corresponding residues in Gram positive clamps occupy a strategic position where a mobile residue is essential for an efficient peptide interaction. (Ec)S346 has a more subtle function that modulates the pocket folding dynamics, while the equivalent residue in B. subtilis is essential for polymerase activity and might therefore be a Gram positive-specific molecular marker. Finally, the peptide binds through an induced-fit process to Gram negative and positive pockets, but the complex stability varies according to a pocket-specific network of interactions.
Interaction of a Model Peptide on Gram Negative and Gram Positive Bacterial Sliding Clamps.,Andre C, Martiel I, Wolff P, Landolfo M, Lorber B, Silva da Veiga C, Dejaegere A, Dumas P, Guichard G, Olieric V, Wagner J, Burnouf DY ACS Infect Dis. 2019 Apr 5. doi: 10.1021/acsinfecdis.9b00089. PMID:30912430[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Andre C, Martiel I, Wolff P, Landolfo M, Lorber B, Silva da Veiga C, Dejaegere A, Dumas P, Guichard G, Olieric V, Wagner J, Burnouf DY. Interaction of a Model Peptide on Gram Negative and Gram Positive Bacterial Sliding Clamps. ACS Infect Dis. 2019 Apr 5. doi: 10.1021/acsinfecdis.9b00089. PMID:30912430 doi:http://dx.doi.org/10.1021/acsinfecdis.9b00089
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