5mmd: Difference between revisions
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==TMB-1. Structural insights into TMB-1 and the role of residue 119 and 228 in substrate and inhibitor binding== | |||
<StructureSection load='5mmd' size='340' side='right'caption='[[5mmd]], [[Resolution|resolution]] 1.75Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5mmd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_baumannii Acinetobacter baumannii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MMD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MMD 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]] 1.75Å</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=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=5mmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mmd OCA], [https://pdbe.org/5mmd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mmd RCSB], [https://www.ebi.ac.uk/pdbsum/5mmd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mmd ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/T2HNV0_ACIBA T2HNV0_ACIBA] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Metallo-beta-lactamases (MBLs) threaten the effectiveness of beta-lactam antibiotics, including carbapenems, and are a concern for global public health. beta-Lactam/beta-lactamase inhibitor combinations active against class A and class D carbapenemases are used, but no clinically useful MBL inhibitor is currently available. Tripoli metallo-beta-lactamase-1 (TMB-1) and TMB-2 are members of MBL subclass B1a, where TMB-2 is an S228P variant of TMB-1. The role of S228P was studied by comparisons of TMB-1 and TMB-2, and E119 was investigated through the construction of site-directed mutants of TMB-1, E119Q, E119S, and E119A (E119Q/S/A). All TMB variants were characterized through enzyme kinetic studies. Thermostability and crystallization analyses of TMB-1 were performed. Thiol-based inhibitors were investigated by determining the 50% inhibitory concentrations (IC50) and binding using surface plasmon resonance (SPR) for analysis of TMB-1. Thermostability measurements found TMB-1 to be stabilized by high NaCl concentrations. Steady-state enzyme kinetics analyses found substitutions of E119, in particular, substitutions associated with the penicillins, to affect hydrolysis to some extent. TMB-2 with S228P showed slightly reduced catalytic efficiency compared to TMB-1. The IC50 levels of the new thiol-based inhibitors were 0.66 muM (inhibitor 2a) and 0.62 muM (inhibitor 2b), and the equilibrium dissociation constant (KD ) of inhibitor 2a was 1.6 muM; thus, both were more potent inhibitors than l-captopril (IC50 = 47 muM; KD = 25 muM). The crystal structure of TMB-1 was resolved to 1.75 A. Modeling of inhibitor 2b in the TMB-1 active site suggested that the presence of the W64 residue results in T-shaped pi-pi stacking and R224 cation-pi interactions with the phenyl ring of the inhibitor. In sum, the results suggest that residues 119 and 228 affect the catalytic efficiency of TMB-1 and that inhibitors 2a and 2b are more potent inhibitors for TMB-1 than l-captopril. | |||
Structural Insights into TMB-1 and the Role of Residues 119 and 228 in Substrate and Inhibitor Binding.,Skagseth S, Christopeit T, Akhter S, Bayer A, Samuelsen O, Leiros HS Antimicrob Agents Chemother. 2017 Jul 25;61(8). pii: e02602-16. doi:, 10.1128/AAC.02602-16. Print 2017 Aug. PMID:28559248<ref>PMID:28559248</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 5mmd" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Beta-lactamase 3D structures|Beta-lactamase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Acinetobacter baumannii]] | |||
[[Category: Large Structures]] | |||
[[Category: Akhter S]] | |||
[[Category: Bayer A]] | |||
[[Category: Christopeit T]] | |||
[[Category: Leiros H-KS]] | |||
[[Category: Samuelsen O]] | |||
[[Category: Skagseth S]] | |||
Latest revision as of 20:38, 8 November 2023
TMB-1. Structural insights into TMB-1 and the role of residue 119 and 228 in substrate and inhibitor bindingTMB-1. Structural insights into TMB-1 and the role of residue 119 and 228 in substrate and inhibitor binding
Structural highlights
FunctionPublication Abstract from PubMedMetallo-beta-lactamases (MBLs) threaten the effectiveness of beta-lactam antibiotics, including carbapenems, and are a concern for global public health. beta-Lactam/beta-lactamase inhibitor combinations active against class A and class D carbapenemases are used, but no clinically useful MBL inhibitor is currently available. Tripoli metallo-beta-lactamase-1 (TMB-1) and TMB-2 are members of MBL subclass B1a, where TMB-2 is an S228P variant of TMB-1. The role of S228P was studied by comparisons of TMB-1 and TMB-2, and E119 was investigated through the construction of site-directed mutants of TMB-1, E119Q, E119S, and E119A (E119Q/S/A). All TMB variants were characterized through enzyme kinetic studies. Thermostability and crystallization analyses of TMB-1 were performed. Thiol-based inhibitors were investigated by determining the 50% inhibitory concentrations (IC50) and binding using surface plasmon resonance (SPR) for analysis of TMB-1. Thermostability measurements found TMB-1 to be stabilized by high NaCl concentrations. Steady-state enzyme kinetics analyses found substitutions of E119, in particular, substitutions associated with the penicillins, to affect hydrolysis to some extent. TMB-2 with S228P showed slightly reduced catalytic efficiency compared to TMB-1. The IC50 levels of the new thiol-based inhibitors were 0.66 muM (inhibitor 2a) and 0.62 muM (inhibitor 2b), and the equilibrium dissociation constant (KD ) of inhibitor 2a was 1.6 muM; thus, both were more potent inhibitors than l-captopril (IC50 = 47 muM; KD = 25 muM). The crystal structure of TMB-1 was resolved to 1.75 A. Modeling of inhibitor 2b in the TMB-1 active site suggested that the presence of the W64 residue results in T-shaped pi-pi stacking and R224 cation-pi interactions with the phenyl ring of the inhibitor. In sum, the results suggest that residues 119 and 228 affect the catalytic efficiency of TMB-1 and that inhibitors 2a and 2b are more potent inhibitors for TMB-1 than l-captopril. Structural Insights into TMB-1 and the Role of Residues 119 and 228 in Substrate and Inhibitor Binding.,Skagseth S, Christopeit T, Akhter S, Bayer A, Samuelsen O, Leiros HS Antimicrob Agents Chemother. 2017 Jul 25;61(8). pii: e02602-16. doi:, 10.1128/AAC.02602-16. Print 2017 Aug. PMID:28559248[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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