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| | ==Crystal structure of the DNA polymerase III subunit beta from Acinetobacter baumannii== | | ==Crystal structure of the DNA polymerase III subunit beta from Acinetobacter baumannii== |
| - | <StructureSection load='6ap4' size='340' side='right' caption='[[6ap4]], [[Resolution|resolution]] 2.95Å' scene=''> | + | <StructureSection load='6ap4' size='340' side='right'caption='[[6ap4]], [[Resolution|resolution]] 2.95Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6ap4]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Aciba Aciba]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AP4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AP4 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6ap4]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_baumannii Acinetobacter baumannii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AP4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6AP4 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.95Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6amq|6amq]], [[6ams|6ams]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dnaN, A7M79_16225, A7M90_19325, A7N09_15145, AB895_1514, ABUW_0002, APD06_07570, APD31_16715, AZE33_00010, B4R90_12040, B9X95_11540, BGC29_18735, BWP00_10155, CAS83_08665, CBI29_00019, CEB38_18810, IX87_14440, LV38_03508 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=470 ACIBA])</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=6ap4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ap4 OCA], [https://pdbe.org/6ap4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ap4 RCSB], [https://www.ebi.ac.uk/pdbsum/6ap4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ap4 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=6ap4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ap4 OCA], [http://pdbe.org/6ap4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ap4 RCSB], [http://www.ebi.ac.uk/pdbsum/6ap4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ap4 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/V5V7W3_ACIBA V5V7W3_ACIBA]] 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.[PIRNR:PIRNR000804] | + | [https://www.uniprot.org/uniprot/V5V7W3_ACIBA V5V7W3_ACIBA] 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.[PIRNR:PIRNR000804] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==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: Aciba]] | + | [[Category: Acinetobacter baumannii]] |
| - | [[Category: McGrath, A E]] | + | [[Category: Large Structures]] |
| - | [[Category: Oakley, A J]] | + | [[Category: McGrath AE]] |
| - | [[Category: Dna binding]] | + | [[Category: Oakley AJ]] |
| - | [[Category: Dna directed dna polymerase activity]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
V5V7W3_ACIBA 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.[PIRNR:PIRNR000804]
Publication Abstract from PubMed
Bacterial sliding clamps bind to DNA and act as protein-protein interaction hubs for several proteins involved in DNA replication and repair. The partner proteins all bind to a common pocket on sliding clamps via conserved linear peptide sequence motifs, which suggest the pocket as an attractive target for development of new antibiotics. Herein we report the X-ray crystal structures and biochemical characterization of beta sliding clamps from the Gram-negative pathogens Pseudomonas aeruginosa, Acinetobacter baumannii and Enterobacter cloacae. The structures reveal close similarity between the pathogen and Escherichia coli clamps and similar patterns of binding to linear clamp-binding motif peptides. The results suggest that linear motif-sliding clamp interactions are well conserved and an antibiotic targeting the sliding clamp should have broad-spectrum activity against Gram-negative pathogens.
Crystal structures and biochemical characterization of DNA sliding clamps from three Gram-negative bacterial pathogens.,McGrath AE, Martyn AP, Whittell LR, Dawes FE, Beck JL, Dixon NE, Kelso MJ, Oakley AJ J Struct Biol. 2018 Oct 23. pii: S1047-8477(18)30281-8. doi:, 10.1016/j.jsb.2018.10.008. PMID:30366028[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ McGrath AE, Martyn AP, Whittell LR, Dawes FE, Beck JL, Dixon NE, Kelso MJ, Oakley AJ. Crystal structures and biochemical characterization of DNA sliding clamps from three Gram-negative bacterial pathogens. J Struct Biol. 2018 Oct 23. pii: S1047-8477(18)30281-8. doi:, 10.1016/j.jsb.2018.10.008. PMID:30366028 doi:http://dx.doi.org/10.1016/j.jsb.2018.10.008
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