|
|
| Line 3: |
Line 3: |
| | <StructureSection load='4tsz' size='340' side='right'caption='[[4tsz]], [[Resolution|resolution]] 2.00Å' scene=''> | | <StructureSection load='4tsz' size='340' side='right'caption='[[4tsz]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4tsz]] is a 32 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TSZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TSZ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4tsz]] is a 32 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa] 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=4TSZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4TSZ FirstGlance]. <br> |
| - | </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>, <scene name='pdbligand=ZCL:3,4-DICHLORO-L-PHENYLALANINE'>ZCL</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=ALC:2-AMINO-3-CYCLOHEXYL-PROPIONIC+ACID'>ALC</scene>, <scene name='pdbligand=ZCL:3,4-DICHLORO-L-PHENYLALANINE'>ZCL</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=4tsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tsz OCA], [https://pdbe.org/4tsz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4tsz RCSB], [https://www.ebi.ac.uk/pdbsum/4tsz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4tsz 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=4tsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tsz OCA], [http://pdbe.org/4tsz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4tsz RCSB], [http://www.ebi.ac.uk/pdbsum/4tsz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4tsz ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/V4MZL6_PSEAI 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] | + | [https://www.uniprot.org/uniprot/DPO3B_PSEAE DPO3B_PSEAE] 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] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 21: |
Line 20: |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[DNA polymerase|DNA polymerase]] | + | *[[DNA polymerase 3D structures|DNA polymerase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: DNA-directed DNA polymerase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Burnouf, D]] | + | [[Category: Pseudomonas aeruginosa]] |
| - | [[Category: Ennifar, E]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Olieric, V]] | + | [[Category: Burnouf D]] |
| - | [[Category: Wolff, P]] | + | [[Category: Ennifar E]] |
| - | [[Category: Transferase]]
| + | [[Category: Olieric V]] |
| | + | [[Category: Wolff P]] |
| Structural highlights
Function
DPO3B_PSEAE 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]
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.
See Also
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
|
