3zkd: Difference between revisions
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<StructureSection load='3zkd' size='340' side='right'caption='[[3zkd]], [[Resolution|resolution]] 2.95Å' scene=''> | <StructureSection load='3zkd' size='340' side='right'caption='[[3zkd]], [[Resolution|resolution]] 2.95Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3zkd]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[3zkd]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZKD 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]] 2.95Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=3zkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zkd OCA], [https://pdbe.org/3zkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zkd RCSB], [https://www.ebi.ac.uk/pdbsum/3zkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zkd 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=3zkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zkd OCA], [https://pdbe.org/3zkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zkd RCSB], [https://www.ebi.ac.uk/pdbsum/3zkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zkd ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/GYRB_MYCTU GYRB_MYCTU] 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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</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Agrawal | [[Category: Mycobacterium tuberculosis]] | ||
[[Category: Aubry | [[Category: Agrawal A]] | ||
[[Category: Bax | [[Category: Aubry A]] | ||
[[Category: Hann | [[Category: Bax B]] | ||
[[Category: Mayer | [[Category: Hann M]] | ||
[[Category: Mossakowska | [[Category: Mayer C]] | ||
[[Category: Petrella | [[Category: Mossakowska D]] | ||
[[Category: Roue | [[Category: Petrella S]] | ||
[[Category: Spitzfaden | [[Category: Roue M]] | ||
[[Category: Volker | [[Category: Spitzfaden C]] | ||
[[Category: Volker C]] | |||
Latest revision as of 14:04, 20 December 2023
CRYSTAL STRUCTURE OF THE ATPASE REGION OF Mycobacterium tuberculosis GyrB WITH AMPPNPCRYSTAL STRUCTURE OF THE ATPASE REGION OF Mycobacterium tuberculosis GyrB WITH AMPPNP
Structural highlights
FunctionGYRB_MYCTU 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 PubMedDNA gyrase, a type II topoisomerase, regulates DNA topology by creating a double-stranded break in one DNA-duplex and transporting another DNA duplex (T-DNA) through this break. The ATPase domains dimerise, in the presence of ATP, to trap the T-DNA segment. Hydrolysis of only one of the two ATPs, and release of the resulting inorganic phosphate, is rate-limiting in DNA strand passage. A long unresolved puzzle is how the non-hydrolysable ATP analogue AMPPNP can catalyse one round of DNA strand passage without inorganic phosphate release. Here we discuss two crystal structures of the Mycobacterium tuberculosis DNA gyrase ATPase domain: one complexed with AMPPCP was unexpectedly monomeric, the other an AMPPNP complex crystallised as a dimer. In the AMPPNP structure the unprotonated nitrogen (P-N=P imino) accepts hydrogen bonds from a well ordered 'ATP-lid', which is known to be required for dimerisation. The equivalent CH2 group, in AMPPCP, cannot accept hydrogen bonds, leaving the 'ATP-lid' region disordered. Further analysis suggested that AMPPNP can be converted from imino (P-N=P) form to the imido form (P-NH-P) during the catalytic cycle. A main-chain NH is proposed to move to either protonate AMPP-N=P to AMPP-NH-P, or to protonate ATP to initiate ATP hydrolysis. This suggests a novel dissociative mechanism for ATP hydrolysis that could be applicable not only to GHKL phosphotransfereses, but also to unrelated ATPases and GTPases such as Ras. Based on the domain orientation in our AMPPCP structure we propose a mechanochemical scheme to explain how ATP hydrolysis is coupled to domain motion. Mycobacterium tuberculosis DNA gyrase ATPase domain structures suggest a dissociative mechanism that explains how ATP hydrolysis is coupled to domain motion.,Agrawal A, Roue M, Spitzfaden C, Petrella S, Aubry A, Hann MM, Bax B, Mayer C Biochem J. 2013 Sep 9. PMID:24015710[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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