4jpm: Difference between revisions

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~~'''Unreleased structure'''~~

~~The entry~~ 4jpm is ~~ON HOLD until Paper~~ Publication

==Structure of SHV-1 beta-lactamase in complex with the 7-alkylidenecephalosporin DCM-1-10 at 1.14 Ang resolution==

== Structural highlights ==

<table><tr><td colspan='2'>[[4jpm]] is a 1 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=4JPM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JPM FirstGlance]. <br>

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.14Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1OG:7-ALKYLIDENECEPHALOSPORIN+DCM-1-10,+BOUND+FORM'>1OG</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MA4:CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE'>MA4</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=4jpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jpm OCA], [https://pdbe.org/4jpm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jpm RCSB], [https://www.ebi.ac.uk/pdbsum/4jpm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jpm ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/BLA1_KLEPN BLA1_KLEPN]

== Publication Abstract from PubMed ==

The inhibition of the class A SHV-1 beta-lactamase by 7-(tert-butoxycarbonyl)methylidenecephalosporin sulfone was examined kinetically, spectroscopically, and crystallographically. An 1.14A X-ray crystal structure shows that the stable acyl-enzyme, which incorporates an eight-membered ring, is a covalent derivative of Ser70 linked to the 7-carboxy group of 2-H-5,8-dihydro-1,1-dioxo-1,5-thiazocine-4,7-dicarboxylic acid. A cephalosporin-derived enzyme complex of this type is unprecedented and the rearrangement leading to its formation may offer new possibilities for inhibitor design. The observed acyl-enzyme derives its stability from the resonance stabilization conveyed by the -aminoacrylate (i.e. vinylogous urethane) functionality as there is relatively little interaction of the eight-membered ring with active site residues. Two mechanistic schemes are proposed, differing in whether, subsequent to acylation of the active site serine and opening of the beta-lactam, the resultant dihydrothiazine fragments on its own, or is assisted by an adjacent nucleophilic atom, in the form of the carbonyl oxygen of the C7 tert-butyloxycarbonyl group. This compound was also found to be a submicromolar inhibitor of the class C ADC-7 and PDC-3 beta-lactamases.

~~Authors~~: Rodkey, ~~E.A.~~, van den Akker, F.

beta-Lactamase Inhibition by 7-Alkylidenecephalosporin Sulfones: Allylic Transposition and Formation of an Unprecedented Stabilized Acyl-Enzyme.,Rodkey EA, McLeod DC, Bethel CR, Smith KM, Xu Y, Chai W, Che T, Carey PR, Bonomo RA, van den Akker F, Buynak JD J Am Chem Soc. 2013 Nov 12. PMID:24219313<ref>PMID:24219313</ref>

~~Description: Structure~~ of ~~SHV~~-~~1 beta~~-lactamase ~~in complex with the 7~~-~~alkylidenecephalosporin DCM-1-10 at 1.14 Ang resolution~~

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

</div>

==See Also==

*[[Beta-lactamase 3D structures|Beta-lactamase 3D structures]]

== References ==

__TOC__

</StructureSection>

[[Category: Klebsiella pneumoniae]]

[[Category: Large Structures]]

[[Category: Rodkey EA]]

[[Category: Van den Akker F]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 4jpm is ON HOLD  until Paper Publication
+==Structure of SHV-1 beta-lactamase in complex with the 7-alkylidenecephalosporin DCM-1-10 at 1.14 Ang resolution==
+<StructureSection load='4jpm' size='340' side='right'caption='[[4jpm]], [[Resolution|resolution]] 1.14&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4jpm]] is a 1 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=4JPM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JPM FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.14&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1OG:7-ALKYLIDENECEPHALOSPORIN+DCM-1-10,+BOUND+FORM'>1OG</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MA4:CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE'>MA4</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=4jpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jpm OCA], [https://pdbe.org/4jpm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jpm RCSB], [https://www.ebi.ac.uk/pdbsum/4jpm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jpm ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/BLA1_KLEPN BLA1_KLEPN]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The inhibition of the class A SHV-1 beta-lactamase by 7-(tert-butoxycarbonyl)methylidenecephalosporin sulfone was examined kinetically, spectroscopically, and crystallographically. An 1.14A X-ray crystal structure shows that the stable acyl-enzyme, which incorporates an eight-membered ring, is a covalent derivative of Ser70 linked to the 7-carboxy group of 2-H-5,8-dihydro-1,1-dioxo-1,5-thiazocine-4,7-dicarboxylic acid. A cephalosporin-derived enzyme complex of this type is unprecedented and the rearrangement leading to its formation may offer new possibilities for inhibitor design. The observed acyl-enzyme derives its stability from the resonance stabilization conveyed by the -aminoacrylate (i.e. vinylogous urethane) functionality as there is relatively little interaction of the eight-membered ring with active site residues. Two mechanistic schemes are proposed, differing in whether, subsequent to acylation of the active site serine and opening of the beta-lactam, the resultant dihydrothiazine fragments on its own, or is assisted by an adjacent nucleophilic atom, in the form of the carbonyl oxygen of the C7 tert-butyloxycarbonyl group. This compound was also found to be a submicromolar inhibitor of the class C ADC-7 and PDC-3 beta-lactamases.
-Authors: Rodkey, E.A., van den Akker, F.
+beta-Lactamase Inhibition by 7-Alkylidenecephalosporin Sulfones: Allylic Transposition and Formation of an Unprecedented Stabilized Acyl-Enzyme.,Rodkey EA, McLeod DC, Bethel CR, Smith KM, Xu Y, Chai W, Che T, Carey PR, Bonomo RA, van den Akker F, Buynak JD J Am Chem Soc. 2013 Nov 12. PMID:24219313<ref>PMID:24219313</ref>
-Description: Structure of SHV-1 beta-lactamase in complex with the 7-alkylidenecephalosporin DCM-1-10 at 1.14 Ang resolution
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 4jpm" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Beta-lactamase 3D structures|Beta-lactamase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Klebsiella pneumoniae]]
+[[Category: Large Structures]]
+[[Category: Rodkey EA]]
+[[Category: Van den Akker F]]