8akm: Difference between revisions
No edit summary |
No edit summary |
||
| (2 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
==Acyl-enzyme complex of ertapenem bound to deacylation mutant KPC-2 (E166Q)== | |||
<StructureSection load='8akm' size='340' side='right'caption='[[8akm]], [[Resolution|resolution]] 1.25Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[8akm]] 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=8AKM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8AKM 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]] 1.25Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=N9X:(2~{S},3~{R},4~{R})-4-[(3~{S},5~{R})-5-[(4-carboxyphenyl)carbamoyl]pyrrolidin-3-yl]sulfanyl-3-methyl-2-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2~{H}-pyrrole-5-carboxylic+acid'>N9X</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=8akm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8akm OCA], [https://pdbe.org/8akm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8akm RCSB], [https://www.ebi.ac.uk/pdbsum/8akm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8akm ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/BLKPC_KLEPN BLKPC_KLEPN] Hydrolyzes carbapenems, penicillins, cephalosporins and monobactams with varying efficiency. | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
KPC-2 (Klebsiella pneumoniae carbapenemase-2) is a globally disseminated serine-beta-lactamase (SBL) responsible for extensive beta-lactam antibiotic resistance in Gram-negative pathogens. SBLs inactivate beta-lactams via a mechanism involving a hydrolytically labile covalent acyl-enzyme intermediate. Carbapenems, the most potent beta-lactams, evade the activity of many SBLs by forming long-lived inhibitory acyl-enzymes; however, carbapenemases such as KPC-2 efficiently deacylate carbapenem acyl-enzymes. We present high-resolution (1.25-1.4 A) crystal structures of KPC-2 acyl-enzymes with representative penicillins (ampicillin), cephalosporins (cefalothin), and carbapenems (imipenem, meropenem, and ertapenem) obtained utilizing an isosteric deacylation-deficient mutant (E166Q). The mobility of the Omega-loop (residues 165-170) negatively correlates with antibiotic turnover rates (k(cat)), highlighting the role of this region in positioning catalytic residues for efficient hydrolysis of different beta-lactams. Carbapenem-derived acyl-enzyme structures reveal the predominance of the Delta1-(2R) imine rather than the Delta2 enamine tautomer. Quantum mechanics/molecular mechanics molecular dynamics simulations of KPC-2:meropenem acyl-enzyme deacylation used an adaptive string method to differentiate the reactivity of the two isomers. These identify the Delta1-(2R) isomer as having a significantly (7 kcal/mol) higher barrier than the Delta2 tautomer for the (rate-determining) formation of the tetrahedral deacylation intermediate. Deacylation is therefore likely to proceed predominantly from the Delta2, rather than the Delta1-(2R) acyl-enzyme, facilitated by tautomer-specific differences in hydrogen-bonding networks involving the carbapenem C-3 carboxylate and the deacylating water and stabilization by protonated N-4, accumulating a negative charge on the Delta2 enamine-derived oxyanion. Taken together, our data show how the flexible Omega-loop helps confer broad-spectrum activity upon KPC-2, while carbapenemase activity stems from efficient deacylation of the Delta2-enamine acyl-enzyme tautomer. | |||
Tautomer-Specific Deacylation and Omega-Loop Flexibility Explain the Carbapenem-Hydrolyzing Broad-Spectrum Activity of the KPC-2 beta-Lactamase.,Tooke CL, Hinchliffe P, Beer M, Zinovjev K, Colenso CK, Schofield CJ, Mulholland AJ, Spencer J J Am Chem Soc. 2023 Apr 5;145(13):7166-7180. doi: 10.1021/jacs.2c12123. Epub 2023 , Mar 27. PMID:36972204<ref>PMID:36972204</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 8akm" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Klebsiella pneumoniae]] | |||
[[Category: Large Structures]] | |||
[[Category: Hinchliffe P]] | |||
[[Category: Spencer J]] | |||
[[Category: Tooke CL]] | |||
Latest revision as of 17:20, 6 November 2024
Acyl-enzyme complex of ertapenem bound to deacylation mutant KPC-2 (E166Q)Acyl-enzyme complex of ertapenem bound to deacylation mutant KPC-2 (E166Q)
Structural highlights
FunctionBLKPC_KLEPN Hydrolyzes carbapenems, penicillins, cephalosporins and monobactams with varying efficiency. Publication Abstract from PubMedKPC-2 (Klebsiella pneumoniae carbapenemase-2) is a globally disseminated serine-beta-lactamase (SBL) responsible for extensive beta-lactam antibiotic resistance in Gram-negative pathogens. SBLs inactivate beta-lactams via a mechanism involving a hydrolytically labile covalent acyl-enzyme intermediate. Carbapenems, the most potent beta-lactams, evade the activity of many SBLs by forming long-lived inhibitory acyl-enzymes; however, carbapenemases such as KPC-2 efficiently deacylate carbapenem acyl-enzymes. We present high-resolution (1.25-1.4 A) crystal structures of KPC-2 acyl-enzymes with representative penicillins (ampicillin), cephalosporins (cefalothin), and carbapenems (imipenem, meropenem, and ertapenem) obtained utilizing an isosteric deacylation-deficient mutant (E166Q). The mobility of the Omega-loop (residues 165-170) negatively correlates with antibiotic turnover rates (k(cat)), highlighting the role of this region in positioning catalytic residues for efficient hydrolysis of different beta-lactams. Carbapenem-derived acyl-enzyme structures reveal the predominance of the Delta1-(2R) imine rather than the Delta2 enamine tautomer. Quantum mechanics/molecular mechanics molecular dynamics simulations of KPC-2:meropenem acyl-enzyme deacylation used an adaptive string method to differentiate the reactivity of the two isomers. These identify the Delta1-(2R) isomer as having a significantly (7 kcal/mol) higher barrier than the Delta2 tautomer for the (rate-determining) formation of the tetrahedral deacylation intermediate. Deacylation is therefore likely to proceed predominantly from the Delta2, rather than the Delta1-(2R) acyl-enzyme, facilitated by tautomer-specific differences in hydrogen-bonding networks involving the carbapenem C-3 carboxylate and the deacylating water and stabilization by protonated N-4, accumulating a negative charge on the Delta2 enamine-derived oxyanion. Taken together, our data show how the flexible Omega-loop helps confer broad-spectrum activity upon KPC-2, while carbapenemase activity stems from efficient deacylation of the Delta2-enamine acyl-enzyme tautomer. Tautomer-Specific Deacylation and Omega-Loop Flexibility Explain the Carbapenem-Hydrolyzing Broad-Spectrum Activity of the KPC-2 beta-Lactamase.,Tooke CL, Hinchliffe P, Beer M, Zinovjev K, Colenso CK, Schofield CJ, Mulholland AJ, Spencer J J Am Chem Soc. 2023 Apr 5;145(13):7166-7180. doi: 10.1021/jacs.2c12123. Epub 2023 , Mar 27. PMID:36972204[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
|
| ||||||||||||||||||