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==Crystal structure of NDM-12 metallo-beta-lactamase in complex with hydrolyzed ampicillin== | ==Crystal structure of NDM-12 metallo-beta-lactamase in complex with hydrolyzed ampicillin== | ||
<StructureSection load='6ol8' size='340' side='right'caption='[[6ol8]]' scene=''> | <StructureSection load='6ol8' size='340' side='right'caption='[[6ol8]], [[Resolution|resolution]] 2.10Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OL8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6OL8 FirstGlance]. <br> | <table><tr><td colspan='2'>[[6ol8]] 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=6OL8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6OL8 FirstGlance]. <br> | ||
</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=6ol8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ol8 OCA], [http://pdbe.org/6ol8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ol8 RCSB], [http://www.ebi.ac.uk/pdbsum/6ol8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ol8 ProSAT]</span></td></tr> | </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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=ZZ7:(2R,4S)-2-[(R)-{[(2R)-2-AMINO-2-PHENYLACETYL]AMINO}(CARBOXY)METHYL]-5,5-DIMETHYL-1,3-THIAZOLIDINE-4-CARBOXYLIC+ACID'>ZZ7</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6ogo|6ogo]]</td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">blaNDM-12 ([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'>[http://proteopedia.org/fgij/fg.htm?mol=6ol8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ol8 OCA], [http://pdbe.org/6ol8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ol8 RCSB], [http://www.ebi.ac.uk/pdbsum/6ol8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ol8 ProSAT]</span></td></tr> | |||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Two accessory loop regions that are present in numerous variants of New Delhi metallo-beta-lactamases (NDM) are important for the enzymatic activity. The first one is a flexible loop L3 that is located near the active site and is thought to play an important role in the catalytic process. The second region, Omega loop is located close to a structural element that coordinates two essential zinc ions. Both loops are not involved in any specific interactions with a substrate. Herein, we investigated how the length and hydrophobicity of loop L3 influence the enzymatic activity of NDMs, by analyzing mutants of NDM-1 with various deletions/point mutations within the L3 loop. We also investigated NDM variants with sequence variations/artificial deletions within the Omega loop. For all these variants we determined kinetic parameters for the hydrolysis of ampicillin, imipenem, and a chromogenic cephalosporin (CENTA). None of the mutations in the L3 loop completely abolished the enzymatic activity of NDM-1. Our results suggest that various elements of the loop play different roles in the hydrolysis of different substrates and the flexibility of the loop seems necessary to fulfill the requirements imposed by various substrates. Deletions within the Omega loop usually enhanced the enzymatic activity, particularly for the hydrolysis of ampicillin and imipenem. However, the exact role of the Omega loop in the catalytic reaction remains unclear. In our kinetic tests, the NDM enzymes were inhibited in the beta-lactamase reaction by the CENTA substrate. We also present the X-ray crystal structures of the NDM-1, NDM-9 and NDM-12 proteins. | |||
Flexible loops of New Delhi metallo-beta-lactamase modulate its activity towards different substrates.,Raczynska JE, Imiolczyk B, Komorowska M, Sliwiak J, Czyrko-Horczak J, Brzezinski K, Jaskolski M Int J Biol Macromol. 2020 Apr 28;158:104-115. doi:, 10.1016/j.ijbiomac.2020.04.219. PMID:32353499<ref>PMID:32353499</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6ol8" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Bacillus coli migula 1895]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Imiolczyk B]] | [[Category: Imiolczyk, B]] | ||
[[Category: Jaskolski M]] | [[Category: Jaskolski, M]] | ||
[[Category: Raczynska | [[Category: Raczynska, J E]] | ||
[[Category: Hydrolase]] | |||
[[Category: Hydrolase-antibiotic complex]] | |||
[[Category: Metallo-beta-lactamase]] | |||
[[Category: Ndm]] | |||
Revision as of 08:48, 13 May 2020
Crystal structure of NDM-12 metallo-beta-lactamase in complex with hydrolyzed ampicillinCrystal structure of NDM-12 metallo-beta-lactamase in complex with hydrolyzed ampicillin
Structural highlights
Publication Abstract from PubMedTwo accessory loop regions that are present in numerous variants of New Delhi metallo-beta-lactamases (NDM) are important for the enzymatic activity. The first one is a flexible loop L3 that is located near the active site and is thought to play an important role in the catalytic process. The second region, Omega loop is located close to a structural element that coordinates two essential zinc ions. Both loops are not involved in any specific interactions with a substrate. Herein, we investigated how the length and hydrophobicity of loop L3 influence the enzymatic activity of NDMs, by analyzing mutants of NDM-1 with various deletions/point mutations within the L3 loop. We also investigated NDM variants with sequence variations/artificial deletions within the Omega loop. For all these variants we determined kinetic parameters for the hydrolysis of ampicillin, imipenem, and a chromogenic cephalosporin (CENTA). None of the mutations in the L3 loop completely abolished the enzymatic activity of NDM-1. Our results suggest that various elements of the loop play different roles in the hydrolysis of different substrates and the flexibility of the loop seems necessary to fulfill the requirements imposed by various substrates. Deletions within the Omega loop usually enhanced the enzymatic activity, particularly for the hydrolysis of ampicillin and imipenem. However, the exact role of the Omega loop in the catalytic reaction remains unclear. In our kinetic tests, the NDM enzymes were inhibited in the beta-lactamase reaction by the CENTA substrate. We also present the X-ray crystal structures of the NDM-1, NDM-9 and NDM-12 proteins. Flexible loops of New Delhi metallo-beta-lactamase modulate its activity towards different substrates.,Raczynska JE, Imiolczyk B, Komorowska M, Sliwiak J, Czyrko-Horczak J, Brzezinski K, Jaskolski M Int J Biol Macromol. 2020 Apr 28;158:104-115. doi:, 10.1016/j.ijbiomac.2020.04.219. PMID:32353499[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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