1kij
From Proteopedia
(Difference between revisions)
| Line 3: | Line 3: | ||
<StructureSection load='1kij' size='340' side='right'caption='[[1kij]], [[Resolution|resolution]] 2.30Å' scene=''> | <StructureSection load='1kij' size='340' side='right'caption='[[1kij]], [[Resolution|resolution]] 2.30Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[1kij]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/ | + | <table><tr><td colspan='2'>[[1kij]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KIJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KIJ FirstGlance]. <br> |
| - | </td></tr><tr id=' | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3Å</td></tr> |
| - | <tr id=' | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=NOV:NOVOBIOCIN'>NOV</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=1kij FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kij OCA], [https://pdbe.org/1kij PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kij RCSB], [https://www.ebi.ac.uk/pdbsum/1kij PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kij ProSAT]</span></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=1kij FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kij OCA], [https://pdbe.org/1kij PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kij RCSB], [https://www.ebi.ac.uk/pdbsum/1kij PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kij ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
| - | + | [https://www.uniprot.org/uniprot/GYRB_THET8 GYRB_THET8] A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner (PubMed:23804759, PubMed:11850422). It probably also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes (PubMed:11850422). Relaxes negatively supercoiled DNA in an ATP-independent manner (PubMed:23804759, PubMed:11850422). At comparable concentrations T.thermophilus gyrase does not introduce as many negative supercoils into DNA as the E.coli enzyme (PubMed:23804759).<ref>PMID:23804759</ref> Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner. | |
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
| Line 20: | Line 20: | ||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1kij ConSurf]. | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1kij ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | DNA gyrase forms an A(2)B(2) tetramer involved in DNA replication, repair, recombination, and transcription in which the B subunit catalyzes ATP hydrolysis. The Thermus thermophilus and Escherichia coli gyrases are homologues and present the same catalytic activity. When compared with that of the E. coli 43K-5'-adenylyl-beta,gamma-imidodiphosphate complex, the crystal structure of Gyrase B 43K ATPase domain in complex with novobiocin, one of the most potent inhibitors of gyrase shows large conformational changes of the subdomains within the dimer. The stabilization of loop 98-118 closing the active site through dimeric contacts and interaction with domain 2 allows to observe novobiocin-protein interactions that could not be seen in the 24K-inhibitor complexes. Furthermore, this loop adopts a position which defines an "open" conformation of the active site in absence of ATP, in contrast with the "closed" conformation adopted upon ATP binding. All together, these results indicate how the subdomains may propagate conformational changes from the active site and provide crucial information for the design of more specific inhibitors. | ||
| - | |||
| - | An open conformation of the Thermus thermophilus gyrase B ATP-binding domain.,Lamour V, Hoermann L, Jeltsch JM, Oudet P, Moras D J Biol Chem. 2002 May 24;277(21):18947-53. Epub 2002 Feb 15. PMID:11850422<ref>PMID:11850422</ref> | ||
| - | |||
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 1kij" style="background-color:#fffaf0;"></div> | ||
==See Also== | ==See Also== | ||
| Line 36: | Line 27: | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: Flavobacterium thermophilum yoshida and oshima 1971]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: Hoermann | + | [[Category: Thermus thermophilus]] |
| - | [[Category: Jeltsch | + | [[Category: Hoermann L]] |
| - | [[Category: Lamour | + | [[Category: Jeltsch J-M]] |
| - | [[Category: Moras | + | [[Category: Lamour V]] |
| - | [[Category: Oudet | + | [[Category: Moras D]] |
| - | + | [[Category: Oudet P]] | |
| - | + | ||
| - | + | ||
Current revision
Crystal structure of the 43K ATPase domain of Thermus thermophilus gyrase B in complex with novobiocin
| |||||||||||
