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6psg

From Proteopedia

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Crystal Structure of Class D Beta-lactamase OXA-48 with Faropenem

Structural highlights

6psg is a 4 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 2.13Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q6XEC0_KLEPN

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Akhtar A, Pemberton OA, Chen Y. Structural Basis for Substrate Specificity and Carbapenemase Activity of OXA-48 Class D beta-Lactamase. ACS Infect Dis. 2020 Feb 14;6(2):261-271. doi: 10.1021/acsinfecdis.9b00304. Epub , 2020 Jan 7. PMID:31872762 doi:http://dx.doi.org/10.1021/acsinfecdis.9b00304

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6psg"

Categories: Klebsiella pneumoniae | Large Structures | Akhtar A | Chen Y

@@ Line 3: / Line 3: @@
 <StructureSection load='6psg' size='340' side='right'caption='[[6psg]], [[Resolution|resolution]] 2.13&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6psg]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pneumoniae"_(schroeter_1886)_flugge_1886 "bacillus pneumoniae" (schroeter 1886) flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PSG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PSG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6psg]] 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=6PSG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PSG FirstGlance]. <br>
-</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=DGF:(2R,5R)-2-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-5-[(2R)-TETRAHYDROFURAN-2-YL]-2,5-DIHYDRO-1,3-THIAZOLE-4-CARBOXYLIC+ACID'>DGF</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.13&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">blaOXA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=573 "Bacillus pneumoniae" (Schroeter 1886) Flugge 1886])</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=DGF:(2R,5R)-2-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-5-[(2R)-TETRAHYDROFURAN-2-YL]-2,5-DIHYDRO-1,3-THIAZOLE-4-CARBOXYLIC+ACID'>DGF</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=6psg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6psg OCA], [https://pdbe.org/6psg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6psg RCSB], [https://www.ebi.ac.uk/pdbsum/6psg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6psg ProSAT]</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=6psg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6psg OCA], [http://pdbe.org/6psg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6psg RCSB], [http://www.ebi.ac.uk/pdbsum/6psg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6psg ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q6XEC0_KLEPN Q6XEC0_KLEPN]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 25: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Beta-lactamase]]
+[[Category: Klebsiella pneumoniae]]
 [[Category: Large Structures]]
-[[Category: Akhtar, A]]
+[[Category: Akhtar A]]
-[[Category: Chen, Y]]
+[[Category: Chen Y]]
-[[Category: Carbapenem]]
-[[Category: Carbapenemase]]
-[[Category: Hydrolase]]
-[[Category: Hydrolyzed product]]
-[[Category: Substrate]]

6psg

From Proteopedia

Current revision

Crystal Structure of Class D Beta-lactamase OXA-48 with Faropenem

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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