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| | ==CCDBVFI:GYRA14EC== | | ==CCDBVFI:GYRA14EC== |
| - | <StructureSection load='4ely' size='340' side='right' caption='[[4ely]], [[Resolution|resolution]] 1.93Å' scene=''> | + | <StructureSection load='4ely' size='340' side='right'caption='[[4ely]], [[Resolution|resolution]] 1.93Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4ely]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_fischeri"_(beijerinck_1889)_bergey_et_al._1930 "achromobacter fischeri" (beijerinck 1889) bergey et al. 1930] and [http://en.wikipedia.org/wiki/"shigella_paradysenteriae"_weldin_1927 "shigella paradysenteriae" weldin 1927]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3ku8 3ku8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ELY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ELY FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4ely]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aliivibrio_fischeri Aliivibrio fischeri] and [https://en.wikipedia.org/wiki/Shigella_flexneri Shigella flexneri]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3ku8 3ku8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ELY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ELY FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3jsc|3jsc]], [[3jrz|3jrz]], [[4elz|4elz]]</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=4ely FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ely OCA], [https://pdbe.org/4ely PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ely RCSB], [https://www.ebi.ac.uk/pdbsum/4ely PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ely ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">gyrA, GYRASE, S2444, SF2311 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=623 "Shigella paradysenteriae" Weldin 1927]), ccdB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=668 "Achromobacter fischeri" (Beijerinck 1889) Bergey et al. 1930])</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>
| + | |
| - | <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=4ely FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ely OCA], [http://pdbe.org/4ely PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ely RCSB], [http://www.ebi.ac.uk/pdbsum/4ely PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ely ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/GYRA_SHIFL GYRA_SHIFL]] 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). | + | [[https://www.uniprot.org/uniprot/GYRA_SHIFL GYRA_SHIFL]] 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). |
| | <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: Shigella paradysenteriae weldin 1927]] | + | [[Category: Aliivibrio fischeri]] |
| - | [[Category: Buts, L]] | + | [[Category: Large Structures]] |
| - | [[Category: Garcia-Pino, A]] | + | [[Category: Shigella flexneri]] |
| - | [[Category: Greve, H De]] | + | [[Category: Buts L]] |
| - | [[Category: Haesaerts, S]] | + | [[Category: De Greve H]] |
| - | [[Category: Jonge, N De]] | + | [[Category: De Jonge N]] |
| - | [[Category: Lah, J]] | + | [[Category: Garcia-Pino A]] |
| - | [[Category: Loris, R]] | + | [[Category: Haesaerts S]] |
| - | [[Category: Roelants, K]] | + | [[Category: Lah J]] |
| - | [[Category: Simic, R]] | + | [[Category: Loris R]] |
| - | [[Category: Sterckx, Y]] | + | [[Category: Roelants K]] |
| - | [[Category: Alpha+beta]] | + | [[Category: Simic R]] |
| - | [[Category: Topoisomerase]] | + | [[Category: Sterckx Y]] |
| - | [[Category: Toxin-isomerase complex]]
| + | |
| Structural highlights
Function
[GYRA_SHIFL] 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).
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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