3vpe: Difference between revisions
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<StructureSection load='3vpe' size='340' side='right'caption='[[3vpe]], [[Resolution|resolution]] 1.60Å' scene=''> | <StructureSection load='3vpe' size='340' side='right'caption='[[3vpe]], [[Resolution|resolution]] 1.60Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3vpe]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[3vpe]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Serratia_marcescens Serratia marcescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VPE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VPE FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=3vpe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vpe OCA], [https://pdbe.org/3vpe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vpe RCSB], [https://www.ebi.ac.uk/pdbsum/3vpe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vpe ProSAT]</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=3vpe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vpe OCA], [https://pdbe.org/3vpe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vpe RCSB], [https://www.ebi.ac.uk/pdbsum/3vpe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vpe ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/G5ELM3_SERMA G5ELM3_SERMA] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Arakawa | [[Category: Serratia marcescens]] | ||
[[Category: Mori | [[Category: Arakawa Y]] | ||
[[Category: Shibayama | [[Category: Mori S]] | ||
[[Category: Wachino | [[Category: Shibayama K]] | ||
[[Category: Yamaguchi | [[Category: Wachino J]] | ||
[[Category: Yamaguchi Y]] | |||
Latest revision as of 15:31, 8 November 2023
Crystal Structure of Metallo-beta-Lactamase SMB-1Crystal Structure of Metallo-beta-Lactamase SMB-1
Structural highlights
FunctionPublication Abstract from PubMedA novel subclass B3 metallo-beta-lactamase (MBL), SMB-1, recently identified from a Serratia marcescens clinical isolate, showed a higher hydrolytic activity against a wide range of beta-lactams than did the other subclass B3 MBLs, i.e., BJP-1 and FEZ-1, from environmental bacteria. To identify the mechanism underlying the differences in substrate specificity among the subclass B3 MBLs, we determined the structure of SMB-1, using 1.6-A diffraction data. Consequently, we found that SMB-1 reserves a space in the active site to accommodate beta-lactam, even with a bulky R1 side chain, due to a loss of amino acid residues corresponding to F31 and L226 of BJP-1, which protrude into the active site to prevent beta-lactam from binding. The protein also possesses a unique amino acid residue, Q157, which probably plays a role in recognition of beta-lactams via the hydrogen bond interaction, which is missing in BJP-1 and FEZ-1, whose K(m) values for beta-lactams are particularly high. In addition, we determined the mercaptoacetate (MCR)-complexed SMB-1 structure and revealed the mode of its inhibition by MCR: the thiolate group bridges to two zinc ions (Zn1 and Zn2). One of the carboxylate oxygen atoms of MCR makes contact with Zn2 and Ser221, and the other makes contact with T223 and a water molecule. Our results demonstrate the possibility that MCR could be a potent inhibitor for subclass B3 MBLs and that the screening technique using MCR as an inhibitor would be effective for detecting subclass B3 MBL producers. Structural insights into the subclass B3 metallo-beta-lactamase SMB-1 and the mode of inhibition by the common metallo-beta-lactamase inhibitor mercaptoacetate.,Wachino J, Yamaguchi Y, Mori S, Kurosaki H, Arakawa Y, Shibayama K Antimicrob Agents Chemother. 2013 Jan;57(1):101-9. doi: 10.1128/AAC.01264-12., Epub 2012 Oct 15. PMID:23070156[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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