8RWS

KPC-2 G89D/E166Q Mutant in Complex with Meropenem

Summary for 8RWS

• Entry DOI: 10.2210/pdb8rws/pdb
• Descriptor: Carbapenem-hydrolyzing beta-lactamase KPC, SULFATE ION, (2S,3R,4R)-4-[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl-3-methyl-2-[(2S,3R)-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2H-pyrrole-5-carboxylic acid, ... (5 entities in total)
• Functional Keywords: beta-lactamase, carbapenem, antibiotic resistance, antimicrobial protein
• Biological source: Klebsiella pneumoniae
• Total number of polymer chains: 1
• Total formula weight: 31922.83

Authors

Beer, M.,Hinchliffe, P.,Tooke, C.L.,Spencer, J. (deposition date: 2024-02-05, release date: 2025-01-22)

Primary citation

Beer, M.,Oliveira, A.S.F.,Tooke, C.L.,Hinchliffe, P.,Tsz Yan Li, A.,Balega, B.,Spencer, J.,Mulholland, A.J.
Dynamical responses predict a distal site that modulates activity in an antibiotic resistance enzyme.
Chem Sci, 15:17232-17244, 2024

PubMed Abstract: β-Lactamases, which hydrolyse β-lactam antibiotics, are key determinants of antibiotic resistance. Predicting the sites and effects of distal mutations in enzymes is challenging. For β-lactamases, the ability to make such predictions would contribute to understanding activity against, and development of, antibiotics and inhibitors to combat resistance. Here, using dynamical non-equilibrium molecular dynamics (D-NEMD) simulations combined with experiments, we demonstrate that intramolecular communication networks differ in three class A SulpHydryl Variant (SHV)-type β-lactamases. Differences in network architecture and correlated motions link to catalytic efficiency and β-lactam substrate spectrum. Further, the simulations identify a distal residue at position 89 in the clinically important carbapenemase 2 (KPC-2), as a participant in similar networks, suggesting that mutation at this position would modulate enzyme activity. Experimental kinetic, biophysical and structural characterisation of the naturally occurring, but previously biochemically uncharacterised, KPC-2 mutant with several antibiotics and inhibitors reveals significant changes in hydrolytic spectrum, specifically reducing activity towards carbapenems without effecting major structural or stability changes. These results show that D-NEMD simulations can predict distal sites where mutation affects enzyme activity. This approach could have broad application in understanding enzyme evolution, and in engineering of natural and enzymes.

PubMed: 39364073
DOI: 10.1039/d4sc03295k

Experimental method

X-RAY DIFFRACTION (1.09 Å)