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| | ==CCDBVFI:GYRA14VFI== | | ==CCDBVFI:GYRA14VFI== |
| - | <StructureSection load='4elz' size='340' side='right' caption='[[4elz]], [[Resolution|resolution]] 2.20Å' scene=''> | + | <StructureSection load='4elz' size='340' side='right'caption='[[4elz]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4elz]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Aiivibrio_fischeri_mj11 Aiivibrio fischeri mj11] and [http://en.wikipedia.org/wiki/Aliivibrio_fischeri_es114 Aliivibrio fischeri es114]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3kua 3kua]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ELZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ELZ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4elz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aliivibrio_fischeri_ES114 Aliivibrio fischeri ES114] and [https://en.wikipedia.org/wiki/Aliivibrio_fischeri_MJ11 Aliivibrio fischeri MJ11]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3kua 3kua]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ELZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ELZ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3jsc|3jsc]], [[3jrz|3jrz]]</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=4elz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4elz OCA], [https://pdbe.org/4elz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4elz RCSB], [https://www.ebi.ac.uk/pdbsum/4elz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4elz ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">gyrA, VF_1204 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=312309 Aliivibrio fischeri ES114]), CcdB, VFMJ11_A0651 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=388396 Aiivibrio fischeri MJ11])</td></tr>
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| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_topoisomerase_(ATP-hydrolyzing) DNA topoisomerase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.3 5.99.1.3] </span></td></tr>
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| - | <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=4elz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4elz OCA], [http://pdbe.org/4elz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4elz RCSB], [http://www.ebi.ac.uk/pdbsum/4elz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4elz ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/Q5E5J7_VIBF1 Q5E5J7_VIBF1]] DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings (By similarity).[HAMAP-Rule:MF_01897] | + | [[https://www.uniprot.org/uniprot/Q5E5J7_ALIF1 Q5E5J7_ALIF1]] A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner.[HAMAP-Rule:MF_01897] |
| | <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== |
| - | *[[Gyrase|Gyrase]] | + | *[[Gyrase 3D Structures|Gyrase 3D Structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Aiivibrio fischeri mj11]] | + | [[Category: Aliivibrio fischeri ES114]] |
| - | [[Category: Aliivibrio fischeri es114]] | + | [[Category: Aliivibrio fischeri MJ11]] |
| - | [[Category: Buts, L]] | + | [[Category: Large Structures]] |
| - | [[Category: Garcia-Pino, A]] | + | [[Category: Buts L]] |
| - | [[Category: Greve, H De]] | + | [[Category: De Greve H]] |
| - | [[Category: Haesaerts, S]] | + | [[Category: De Jonge N]] |
| - | [[Category: Jonge, N De]] | + | [[Category: Garcia-Pino A]] |
| - | [[Category: Lah, J]] | + | [[Category: Haesaerts S]] |
| - | [[Category: Loris, R]] | + | [[Category: Lah J]] |
| - | [[Category: Roelants, K]] | + | [[Category: Loris R]] |
| - | [[Category: Simic, M]] | + | [[Category: Roelants K]] |
| - | [[Category: Sterckx, Y]] | + | [[Category: Simic M]] |
| - | [[Category: Alpha+beta]]
| + | [[Category: Sterckx Y]] |
| - | [[Category: Topoisomerase]]
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| - | [[Category: Toxin-isomerase complex]]
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| Structural highlights
Function
[Q5E5J7_ALIF1] A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner.[HAMAP-Rule:MF_01897]
Publication Abstract from PubMed
Toxin-antitoxin (TA) modules are small operons associated with stress response of bacteria. F-plasmid CcdB(F) was the first TA toxin for which its target, gyrase, was identified. Plasmidic and chromosomal CcdBs belong to distinct families. Conserved residues crucial for gyrase poisoning activity of plasmidic CcdBs are not conserved among these families. Here we show that the chromosomal CcdB(Vfi) from Vibrio fischeri is an active gyrase poison that interacts with its target via an alternative energetic mechanism. Changes in the GyrA14-binding surface of the Vibrio and F-plasmid CcdB family members illustrate neutral drift where alternative interactions can be used to achieve the same functionality. Differences in affinity between V. fischeri and F-plasmid CcdB for gyrase and their corresponding CcdA antitoxin possibly reflect distinct roles for TA modules located on plasmids and chromosomes.
Alternative interactions define gyrase specificity in the CcdB family.,De Jonge N, Simic M, Buts L, Haesaerts S, Roelants K, Garcia-Pino A, Sterckx Y, De Greve H, Lah J, Loris R Mol Microbiol. 2012 Jun;84(5):965-978. doi: 10.1111/j.1365-2958.2012.08069.x., Epub 2012 May 14. PMID:22582791[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ De Jonge N, Simic M, Buts L, Haesaerts S, Roelants K, Garcia-Pino A, Sterckx Y, De Greve H, Lah J, Loris R. Alternative interactions define gyrase specificity in the CcdB family. Mol Microbiol. 2012 Jun;84(5):965-978. doi: 10.1111/j.1365-2958.2012.08069.x., Epub 2012 May 14. PMID:22582791 doi:10.1111/j.1365-2958.2012.08069.x
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