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| | <StructureSection load='6v7h' size='340' side='right'caption='[[6v7h]], [[Resolution|resolution]] 1.00Å' scene=''> | | <StructureSection load='6v7h' size='340' side='right'caption='[[6v7h]], [[Resolution|resolution]] 1.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6v7h]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V7H OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6V7H FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6v7h]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V7H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6V7H FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4D6:{(3R,6S)-2-HYDROXY-3-[(THIOPHEN-2-YLACETYL)AMINO]-1,2-OXABORINAN-6-YL}ACETIC+ACID'>4D6</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=WXM:2-[(3~{R},6~{S})-2,2-bis(oxidanyl)-3-(2-thiophen-2-ylethanoylamino)-1-oxa-2-boranuidacyclohex-6-yl]ethanoic+acid'>WXM</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4D6:{(3R,6S)-2-HYDROXY-3-[(THIOPHEN-2-YLACETYL)AMINO]-1,2-OXABORINAN-6-YL}ACETIC+ACID'>4D6</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=WXM:2-[(3~{R},6~{S})-2,2-bis(oxidanyl)-3-(2-thiophen-2-ylethanoylamino)-1-oxa-2-boranuidacyclohex-6-yl]ethanoic+acid'>WXM</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">blaCTX-M-14 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=6v7h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v7h OCA], [https://pdbe.org/6v7h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6v7h RCSB], [https://www.ebi.ac.uk/pdbsum/6v7h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6v7h ProSAT]</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://proteopedia.org/fgij/fg.htm?mol=6v7h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v7h OCA], [http://pdbe.org/6v7h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6v7h RCSB], [http://www.ebi.ac.uk/pdbsum/6v7h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6v7h ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q9L5C7_ECOLX Q9L5C7_ECOLX] |
| | <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 6v7h" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6v7h" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Beta-lactamase 3D structures|Beta-lactamase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| - | [[Category: Beta-lactamase]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Chen, Y]] | + | [[Category: Chen Y]] |
| - | [[Category: Pemberton, O A]] | + | [[Category: Pemberton OA]] |
| - | [[Category: Boronate]]
| + | |
| - | [[Category: Esbl]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Inhibitor]]
| + | |
| Structural highlights
6v7h is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
Q9L5C7_ECOLX
Publication Abstract from PubMed
Class A beta-lactamases are a major cause of beta-lactam resistance in Gram-negative bacteria. The recent FDA approved cyclic boronate, vaborbactam, is a reversible covalent inhibitor of class A beta-lactamases including CTX-M extended-spectrum beta-lactamase and KPC carbapenemase, both frequently observed in the clinic. Intriguingly, vaborbactam displayed different binding kinetics and cell-based activity towards these two enzymes, despite their similarity. A 1.0 A crystal structure of CTX-M-14 demonstrates that two catalytic residues, K73 and E166, are positively charged and neutral, respectively. Meanwhile, a 1.25 A crystal structure of KPC-2 revealed a more compact binding mode of vaborbactam versus CTX-M-14, and alternative conformations of W105. Together with kinetic analysis of W105 mutants, the structures demonstrate the influence of this residue and the unusual conformation of the beta3 strand on the inactivation rate, and the stability of the reversible covalent bond with S70. Furthermore, studies of KPC-2 S130G mutant shed light on the different impacts of S130 in the binding of vaborbactam versus avibactam, another recently approved beta-lactamase inhibitor. Taken together, these new data provide valuable insights into the inhibition mechanism of vaborbactam and future development of cyclic boronate inhibitors.
Structural basis and binding kinetics of vaborbactam in class A beta-lactamase inhibition.,Pemberton OA, Tsivkovski R, Totrov M, Lomovskaya O, Chen Y Antimicrob Agents Chemother. 2020 Aug 10. pii: AAC.00398-20. doi:, 10.1128/AAC.00398-20. PMID:32778546[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Pemberton OA, Tsivkovski R, Totrov M, Lomovskaya O, Chen Y. Structural basis and binding kinetics of vaborbactam in class A beta-lactamase inhibition. Antimicrob Agents Chemother. 2020 Aug 10. pii: AAC.00398-20. doi:, 10.1128/AAC.00398-20. PMID:32778546 doi:http://dx.doi.org/10.1128/AAC.00398-20
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