3no0: Difference between revisions
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==Aquifex aeolicus type IIA topoisomerase C-terminal domain== | ==Aquifex aeolicus type IIA topoisomerase C-terminal domain== | ||
<StructureSection load='3no0' size='340' side='right' caption='[[3no0]], [[Resolution|resolution]] 1.30Å' scene=''> | <StructureSection load='3no0' size='340' side='right'caption='[[3no0]], [[Resolution|resolution]] 1.30Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3no0]] is a 3 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3no0]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquae Aquae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NO0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NO0 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>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</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>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aq_980, gyrA, ParC ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aq_980, gyrA, ParC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 AQUAE])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA_topoisomerase_(ATP-hydrolyzing) DNA topoisomerase (ATP-hydrolyzing)], with EC number [https://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'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3no0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3no0 OCA], [https://pdbe.org/3no0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3no0 RCSB], [https://www.ebi.ac.uk/pdbsum/3no0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3no0 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[[ | [[https://www.uniprot.org/uniprot/GYRA_AQUAE GYRA_AQUAE]] 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.[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/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Aquae]] | [[Category: Aquae]] | ||
[[Category: Large Structures]] | |||
[[Category: Berger, J M]] | [[Category: Berger, J M]] | ||
[[Category: Lerman, J C]] | [[Category: Lerman, J C]] | ||
Revision as of 10:06, 12 May 2022
Aquifex aeolicus type IIA topoisomerase C-terminal domainAquifex aeolicus type IIA topoisomerase C-terminal domain
Structural highlights
Function[GYRA_AQUAE] 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.[HAMAP-Rule:MF_01897] Publication Abstract from PubMedBacteria frequently possess two type IIA DNA topoisomerases, gyrase and topo IV, which maintain chromosome topology by variously supercoiling, relaxing, and disentangling DNA. DNA recognition and functional output is thought to be controlled by the C-terminal domain (CTD) of the topoisomerase DNA binding subunit (GyrA/ParC). The deeply rooted organism Aquifex aeolicus encodes one type IIA topoisomerase conflictingly categorized as either DNA gyrase or topo IV. To resolve this enzyme's catalytic properties and heritage, we conducted a series of structural and biochemical studies on the isolated GyrA/ParC CTD and the holoenzyme. Whereas the CTD displays a global structure similar to that seen in bone fide GyrA and ParC paralogs, it lacks a key functional motif (the "GyrA-box") and fails to wrap DNA. Biochemical assays show that the A. aeolicus topoisomerase cannot supercoil DNA, but robustly removes supercoils and decatenates DNA, two hallmark activities of topo IV. Despite these properties, phylogenetic analyses place all functional domains except the CTD squarely within a gyrase lineage, and the A. aeolicus GyrB subunit is capable of supporting supercoiling with Escherichia coli GyrA, but not DNA relaxation with E. coli ParC. Moreover, swapping the A. aeolicus GyrA/ParC CTD with the GyrA CTD from Thermotoga maritima creates an enzyme that negatively supercoils DNA. These findings identify A. aeolicus as the first bacterial species yet found to exist without a functional gyrase, and suggest an evolutionary path for generation of bacterial type IIA paralogs. A naturally chimeric type IIA topoisomerase in Aquifex aeolicus highlights an evolutionary path for the emergence of functional paralogs.,Tretter EM, Lerman JC, Berger JM Proc Natl Acad Sci U S A. 2010 Nov 12. PMID:21076033[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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