7lnq: Difference between revisions
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<StructureSection load='7lnq' size='340' side='right'caption='[[7lnq]], [[Resolution|resolution]] 1.73Å' scene=''> | <StructureSection load='7lnq' size='340' side='right'caption='[[7lnq]], [[Resolution|resolution]] 1.73Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[7lnq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[7lnq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridioides_difficile Clostridioides difficile]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LNQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LNQ FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO2:CARBON+DIOXIDE'>CO2</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NXL:(2S,5R)-1-FORMYL-5-[(SULFOOXY)AMINO]PIPERIDINE-2-CARBOXAMIDE'>NXL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.73Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO2:CARBON+DIOXIDE'>CO2</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NXL:(2S,5R)-1-FORMYL-5-[(SULFOOXY)AMINO]PIPERIDINE-2-CARBOXAMIDE'>NXL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7lnq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lnq OCA], [https://pdbe.org/7lnq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lnq RCSB], [https://www.ebi.ac.uk/pdbsum/7lnq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lnq 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=7lnq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lnq OCA], [https://pdbe.org/7lnq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lnq RCSB], [https://www.ebi.ac.uk/pdbsum/7lnq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lnq ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/A0A160YKM3_CLODI A0A160YKM3_CLODI] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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</div> | </div> | ||
<div class="pdbe-citations 7lnq" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 7lnq" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Beta-lactamase 3D structures|Beta-lactamase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Clostridioides difficile]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Smith | [[Category: Smith CA]] | ||
[[Category: Stewart | [[Category: Stewart NK]] | ||
[[Category: Vakulenko | [[Category: Vakulenko SB]] | ||
Latest revision as of 18:54, 18 October 2023
Structure of the avibactam-CDD-1 3 minute complex in imidazole and MPDStructure of the avibactam-CDD-1 3 minute complex in imidazole and MPD
Structural highlights
FunctionPublication Abstract from PubMedClass D beta-lactamases have risen to notoriety due to their wide spread in bacterial pathogens, propensity to inactivate clinically important beta-lactam antibiotics, and ability to withstand inhibition by the majority of classical beta-lactamase inhibitors. Understanding the catalytic mechanism of these enzymes is thus vitally important for the development of novel antibiotics and inhibitors active against infections caused by antibiotic-resistant bacteria. Here we report an in crystallo time-resolved study of the interaction of the class D beta-lactamase CDD-1 from Clostridioides difficile with the diazobicyclooctane inhibitor, avibactam. We show that the catalytic carboxylated lysine, a residue that is essential for both acylation and deacylation of beta-lactams, is sequestered within an internal sealed pocket of the enzyme. Time-resolved snapshots generated in this study allowed us to observe decarboxylation of the lysine and movement of CO2 and water molecules through a transient channel formed between the lysine pocket and the substrate binding site facilitated by rotation of the side chain of a conserved leucine residue. These studies provide novel insights on avibactam binding to CDD-1 and into the catalytic mechanism of class D beta-lactamases in general. In Crystallo Time-Resolved Interaction of the Clostridioides difficile CDD-1 enzyme with Avibactam Provides New Insights into the Catalytic Mechanism of Class D beta-lactamases.,Stewart NK, Toth M, Stasyuk A, Vakulenko SB, Smith CA ACS Infect Dis. 2021 Apr 28. doi: 10.1021/acsinfecdis.1c00094. PMID:33908775[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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