9h12: Difference between revisions

Latest revision as of 10:24, 3 September 2025

Crystal structure of OXA-48 in complex with nacubactam

Structural highlights

9h12 is a 2 chain structure with sequence from Klebsiella pneumoniae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.51Å
Ligands:	CL, DMS, EDO, GOL, OP0, PEG, PG4, PGE
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

BLO48_KLEPN Class D beta-lactamase which confers resistance to the beta-lactam antibiotics, including amoxicillin, and moderate resistance to cephalosporins and carbapenems such as cephalothin and imipenem; in the DH10B strain of E.coli (PubMed:14693513). Acts via hydrolysis of the beta-lactam ring (PubMed:14693513, PubMed:19477418, PubMed:27073009, PubMed:38161376). Has oxacillin-, cephalothin- and imipenem-hydrolyzing activities (PubMed:14693513, PubMed:19477418, PubMed:27073009, PubMed:38161376).^[1] ^[2] ^[3] ^[4]

References

↑ Poirel L, Héritier C, Tolün V, Nordmann P. Emergence of oxacillinase-mediated resistance to imipenem in Klebsiella pneumoniae. Antimicrob Agents Chemother. 2004 Jan;48(1):15-22. PMID:14693513 doi:10.1128/AAC.48.1.15-22.2004
↑ Docquier JD, Calderone V, De Luca F, Benvenuti M, Giuliani F, Bellucci L, Tafi A, Nordmann P, Botta M, Rossolini GM, Mangani S. Crystal structure of the OXA-48 beta-lactamase reveals mechanistic diversity among class D carbapenemases. Chem Biol. 2009 May 29;16(5):540-7. PMID:19477418 doi:10.1016/j.chembiol.2009.04.010
↑ Stojanoski V, Adamski CJ, Hu L, Mehta SC, Sankaran B, Zwart P, Prasad BV, Palzkill T. Removal of the Side Chain at the Active-Site Serine by a Glycine Substitution Increases the Stability of a Wide Range of Serine beta-Lactamases by Relieving Steric Strain. Biochemistry. 2016 May 3;55(17):2479-90. doi: 10.1021/acs.biochem.6b00056. Epub, 2016 Apr 22. PMID:27073009 doi:https://dx.doi.org/10.1021/acs.biochem.6b00056
↑ Zhou Q, Catalán P, Bell H, Baumann P, Cooke R, Evans R, Yang J, Zhang Z, Zappalà D, Zhang Y, Blackburn GM, He Y, Jin Y. An Ion-Pair Induced Intermediate Complex Captured in Class D Carbapenemase Reveals Chloride Ion as a Janus Effector Modulating Activity. ACS Cent Sci. 2023 Dec 13;9(12):2339-2349. PMID:38161376 doi:10.1021/acscentsci.3c00609

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OCA

[1] Poirel L, Héritier C, Tolün V, Nordmann P. Emergence of oxacillinase-mediated resistance to imipenem in Klebsiella pneumoniae. Antimicrob Agents Chemother. 2004 Jan;48(1):15-22. PMID:14693513 doi:10.1128/AAC.48.1.15-22.2004

[2] Docquier JD, Calderone V, De Luca F, Benvenuti M, Giuliani F, Bellucci L, Tafi A, Nordmann P, Botta M, Rossolini GM, Mangani S. Crystal structure of the OXA-48 beta-lactamase reveals mechanistic diversity among class D carbapenemases. Chem Biol. 2009 May 29;16(5):540-7. PMID:19477418 doi:10.1016/j.chembiol.2009.04.010

[3] Stojanoski V, Adamski CJ, Hu L, Mehta SC, Sankaran B, Zwart P, Prasad BV, Palzkill T. Removal of the Side Chain at the Active-Site Serine by a Glycine Substitution Increases the Stability of a Wide Range of Serine beta-Lactamases by Relieving Steric Strain. Biochemistry. 2016 May 3;55(17):2479-90. doi: 10.1021/acs.biochem.6b00056. Epub, 2016 Apr 22. PMID:27073009 doi:https://dx.doi.org/10.1021/acs.biochem.6b00056

[4] Zhou Q, Catalán P, Bell H, Baumann P, Cooke R, Evans R, Yang J, Zhang Z, Zappalà D, Zhang Y, Blackburn GM, He Y, Jin Y. An Ion-Pair Induced Intermediate Complex Captured in Class D Carbapenemase Reveals Chloride Ion as a Janus Effector Modulating Activity. ACS Cent Sci. 2023 Dec 13;9(12):2339-2349. PMID:38161376 doi:10.1021/acscentsci.3c00609

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[2]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9h12 is ON HOLD  until Paper Publication
+==Crystal structure of OXA-48 in complex with nacubactam==
+<StructureSection load='9h12' size='340' side='right'caption='[[9h12]], [[Resolution|resolution]] 1.51&Aring;' scene=''>
-Authors:
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9h12]] is a 2 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=9H12 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9H12 FirstGlance]. <br>
-Description:
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.51&#8491;</td></tr>
-[[Category: Unreleased Structures]]
+<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=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=OP0:(2S,5R)-N-(2-AMINOETHOXY)-1-FORMYL-5-[(SULFOOXY)AMINO]PIPERIDINE-2-CARBOXAMIDE'>OP0</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=9h12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9h12 OCA], [https://pdbe.org/9h12 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9h12 RCSB], [https://www.ebi.ac.uk/pdbsum/9h12 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9h12 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/BLO48_KLEPN BLO48_KLEPN] Class D beta-lactamase which confers resistance to the beta-lactam antibiotics, including amoxicillin, and moderate resistance to cephalosporins and carbapenems such as cephalothin and imipenem; in the DH10B strain of E.coli (PubMed:14693513). Acts via hydrolysis of the beta-lactam ring (PubMed:14693513, PubMed:19477418, PubMed:27073009, PubMed:38161376). Has oxacillin-, cephalothin- and imipenem-hydrolyzing activities (PubMed:14693513, PubMed:19477418, PubMed:27073009, PubMed:38161376).<ref>PMID:14693513</ref> <ref>PMID:19477418</ref> <ref>PMID:27073009</ref> <ref>PMID:38161376</ref>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Klebsiella pneumoniae]]
+[[Category: Large Structures]]
+[[Category: Goudar KE]]
+[[Category: Hinchliffe P]]
+[[Category: Hoff JF]]
+[[Category: Spencer J]]

9h12: Difference between revisions

Latest revision as of 10:24, 3 September 2025

Crystal structure of OXA-48 in complex with nacubactam

Structural highlights

Function

References

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