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< | ==Aquifex aeolicus type IIA topoisomerase C-terminal domain== | ||
<StructureSection load='3no0' size='340' side='right'caption='[[3no0]], [[Resolution|resolution]] 1.30Å' scene=''> | |||
== Structural highlights == | |||
or the | <table><tr><td colspan='2'>[[3no0]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus_VF5 Aquifex aeolicus VF5]. 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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.3004Å</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='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> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/TOP4A_AQUAE TOP4A_AQUAE] A type II topoisomerase. Despite its similarity to DNA gyrase, this enzyme is not able to supercoil DNA, and instead acts like topoisomerase IV. Relaxes both positively and negatively supercoiled DNA in an ATP-dependent fashion, decatenates interlocked circles. This the first bacteria shown to not contain DNA gyrase, although it has 2 copies of a reverse gyrase that introduces positive supercoils. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner (PubMed:21076033).<ref>PMID:21076033</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Bacteria 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<ref>PMID:21076033</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3no0" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Gyrase 3D Structures|Gyrase 3D Structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Aquifex aeolicus VF5]] | ||
[[Category: Large Structures]] | |||
[[Category: Berger JM]] | |||
== | [[Category: Lerman JC]] | ||
< | [[Category: Tretter EM]] | ||
[[Category: Aquifex aeolicus]] | |||
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Latest revision as of 03:32, 28 December 2023
Aquifex aeolicus type IIA topoisomerase C-terminal domainAquifex aeolicus type IIA topoisomerase C-terminal domain
Structural highlights
FunctionTOP4A_AQUAE A type II topoisomerase. Despite its similarity to DNA gyrase, this enzyme is not able to supercoil DNA, and instead acts like topoisomerase IV. Relaxes both positively and negatively supercoiled DNA in an ATP-dependent fashion, decatenates interlocked circles. This the first bacteria shown to not contain DNA gyrase, although it has 2 copies of a reverse gyrase that introduces positive supercoils. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner (PubMed:21076033).[1] 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[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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