5ndb: Difference between revisions
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<StructureSection load='5ndb' size='340' side='right' caption='[[5ndb]], [[Resolution|resolution]] 2.38Å' scene=''> | <StructureSection load='5ndb' size='340' side='right' caption='[[5ndb]], [[Resolution|resolution]] 2.38Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5ndb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NDB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NDB FirstGlance]. <br> | <table><tr><td colspan='2'>[[5ndb]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NDB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NDB FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8TW:(1~{S},4~{R},5~{S})-7,7-bis(chloranyl)-6,6-bis(oxidanyl)-2$l^{4}-thiabicyclo[3.2.0]hept-2-ene-4-carboxylic+acid'>8TW</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8TW:(1~{S},4~{R},5~{S})-7,7-bis(chloranyl)-6,6-bis(oxidanyl)-2$l^{4}-thiabicyclo[3.2.0]hept-2-ene-4-carboxylic+acid'>8TW</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">spm-1, bla SPM-1, blaSPM-1, CCBH4851_00081, ICEPaeSP_00028 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ndb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ndb OCA], [http://pdbe.org/5ndb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ndb RCSB], [http://www.ebi.ac.uk/pdbsum/5ndb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ndb ProSAT]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ndb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ndb OCA], [http://pdbe.org/5ndb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ndb RCSB], [http://www.ebi.ac.uk/pdbsum/5ndb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ndb ProSAT]</span></td></tr> | ||
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</div> | </div> | ||
<div class="pdbe-citations 5ndb" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 5ndb" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Beta-lactamase|Beta-lactamase]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
Revision as of 08:50, 25 April 2018
Crystal structure of metallo-beta-lactamase SPM-1 complexed with cyclobutanone inhibitorCrystal structure of metallo-beta-lactamase SPM-1 complexed with cyclobutanone inhibitor
Structural highlights
Publication Abstract from PubMedThe most important resistance mechanism to beta-lactam antibiotics involves hydrolysis by two beta-lactamase categories: the nucleophilic serine (SBL) and the metallo- (MBL) beta-lactamases. Cyclobutanones are hydrolytically stable beta-lactam analogues with potential to inhibit both SBLs and MBLs. We describe solution and crystallographic studies on the interaction of a cyclobutanone penem analogue with the clinically important MBL SPM-1. NMR experiments using 19F-labeled SPM-1 imply the cyclobutanone binds to SPM-1 with micromolar affinity. A crystal structure of the SPM-1:cyclobutanone complex reveals binding of the hydrated cyclobutanone via interactions with one of the zinc ions, stabilisation of the hydrate by hydrogen bonding to zinc-bound water, and hydrophobic contacts with aromatic residues. NMR analyses using a 13C-labeled cyclobutanone support assignment of the bound species as the hydrated ketone. The results inform on how MBLs bind substrates and stabilize tetrahedral intermediates. They support further investigations on the use of transition state and/or intermediate analogues as inhibitors of all beta-lactamase classes. Cyclobutanone Mimics of Intermediates in Metallo-beta-Lactamase Catalysis.,Abboud MI, Kosmopoulou M, Krismanich A, Johnson JW, Hinchliffe P, Brem J, Claridge TDW, Spencer J, Schofield C, Dmitrienko GI Chemistry. 2017 Dec 17. doi: 10.1002/chem.201705886. PMID:29250863[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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