6pk0: Difference between revisions
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<StructureSection load='6pk0' size='340' side='right'caption='[[6pk0]], [[Resolution|resolution]] 1.75Å' scene=''> | <StructureSection load='6pk0' size='340' side='right'caption='[[6pk0]], [[Resolution|resolution]] 1.75Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6pk0]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PK0 OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[6pk0]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PK0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PK0 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HIW:(2R,4S)-2-[(1S,2R)-1-CARBOXY-2-HYDROXYPROPYL]-4-[(2-{[(Z)-IMINOMETHYL]AMINO}ETHYL)SULFANYL]-3,4-DIHYDRO-2H-PYRROLE-5-CARBOXYLIC+ACID'>HIW</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]] 1.75Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HIW:(2R,4S)-2-[(1S,2R)-1-CARBOXY-2-HYDROXYPROPYL]-4-[(2-{[(Z)-IMINOMETHYL]AMINO}ETHYL)SULFANYL]-3,4-DIHYDRO-2H-PYRROLE-5-CARBOXYLIC+ACID'>HIW</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></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=6pk0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pk0 OCA], [https://pdbe.org/6pk0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pk0 RCSB], [https://www.ebi.ac.uk/pdbsum/6pk0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pk0 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/Q6XEC0_KLEPN Q6XEC0_KLEPN] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Carbapenem-hydrolyzing class D beta-lactamases (CHDLs) are a diverse family of enzymes that are rapidly becoming the predominant cause of bacterial resistance against beta-lactam antibiotics in many regions of the world. OXA-48, an atypical member of CHDLs, is one of the most frequently observed in the clinic and exhibits a unique substrate profile. We applied X-ray crystallography to OXA-48 complexes with multiple beta-lactam antibiotics to elucidate this enzyme's carbapenemase activity and its preference of imipenem over meropenem and other substrates such as cefotaxime. In particular, we obtained acyl-enzyme complexes of OXA-48 with imipenem, meropenem, faropenem, cefotaxime, and cefoxitin, and a product complex with imipenem. Importantly, the product complex captures a key reaction milestone with the newly generated carboxylate group still in the oxyanion hole, and represents the first such complex with a wild-type serine beta-lactamase. A potential hydrogen bond is observed between the two carboxylate groups from the product and the carbamylated Lys73, representing the stage immediately after the breakage of the acyl-enzyme bond where the product carboxylate would be neutral. The placement of the product carboxylate also illustrates the approximate transient location of the deacylation water that has long eluded structural characterization in class D beta-lactamases. Additionally, comparing the product complex with the acyl-enzyme intermediates provides new insights into the various mechanisms by which specific side chain groups hinder the access of the deacylation water to the acyl-enzyme linkage, especially in meropenem. Taken together, these data offer valuable information on the substrate specificity of OXA-48 and the catalytic mechanism of CHDLs. | |||
Structural Basis for Substrate Specificity and Carbapenemase Activity of OXA-48 Class D beta-Lactamase.,Akhtar A, Pemberton OA, Chen Y ACS Infect Dis. 2020 Feb 14;6(2):261-271. doi: 10.1021/acsinfecdis.9b00304. Epub , 2020 Jan 7. PMID:31872762<ref>PMID:31872762</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6pk0" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Beta-lactamase 3D structures|Beta-lactamase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Klebsiella pneumoniae]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Akhtar | [[Category: Akhtar A]] | ||
[[Category: Chen | [[Category: Chen Y]] | ||