4elz

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (15:04, 14 March 2024) (edit) (undo)
 
(3 intermediate revisions not shown.)
Line 1: Line 1:
 +
==CCDBVFI:GYRA14VFI==
==CCDBVFI:GYRA14VFI==
-
<StructureSection load='4elz' size='340' side='right' caption='[[4elz]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+
<StructureSection load='4elz' size='340' side='right'caption='[[4elz]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[4elz]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Aliivibrio_fischeri Aliivibrio fischeri]. 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><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
-
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3jsc|3jsc]], [[3jrz|3jrz]]</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><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=668 Aliivibrio fischeri]), CcdB, VFMJ11_A0651 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=668 Aliivibrio fischeri])</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><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>
+
</table>
-
<tr><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://www.rcsb.org/pdb/explore.do?structureId=4elz RCSB], [http://www.ebi.ac.uk/pdbsum/4elz PDBsum]</span></td></tr>
+
== Function ==
-
<table>
+
[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;">
+
-
== 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<ref>PMID:22582791</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
==See Also==
==See Also==
-
*[[Gyrase|Gyrase]]
+
*[[Gyrase 3D Structures|Gyrase 3D Structures]]
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Aliivibrio fischeri]]
+
[[Category: Aliivibrio fischeri ES114]]
-
[[Category: Buts, L.]]
+
[[Category: Aliivibrio fischeri MJ11]]
-
[[Category: Garcia-Pino, A.]]
+
[[Category: Large Structures]]
-
[[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, M.]]
+
[[Category: Loris R]]
-
[[Category: Sterckx, Y.]]
+
[[Category: Roelants K]]
-
[[Category: Alpha+beta]]
+
[[Category: Simic M]]
-
[[Category: Topoisomerase]]
+
[[Category: Sterckx Y]]
-
[[Category: Toxin-isomerase complex]]
+

Current revision

CCDBVFI:GYRA14VFI

PDB ID 4elz

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4elz"
Personal tools