4QU3

GES-2 ertapenem acyl-enzyme complex

Summary for 4QU3

• Entry DOI: 10.2210/pdb4qu3/pdb
• Related: 3NI9 3NIA
• Descriptor: Beta-lactamase GES-2, (4R,5S)-3-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid, CALCIUM ION, ... (6 entities in total)
• Functional Keywords: antibiotic resistance, beta-lactamase, hydrolase, ertapenem, hydrolase-antibiotic complex, hydrolase/antibiotic
• Biological source: Pseudomonas aeruginosa
• Total number of polymer chains: 2
• Total formula weight: 64317.61

Authors

Stewart, N.K.,Smith, C.A.,Frase, H.,Black, D.J.,Vakulenko, S.B. (deposition date: 2014-07-10, release date: 2014-12-31, Last modification date: 2024-10-16)

Primary citation

Stewart, N.K.,Smith, C.A.,Frase, H.,Black, D.J.,Vakulenko, S.B.
Kinetic and Structural Requirements for Carbapenemase Activity in GES-Type beta-Lactamases.
Biochemistry, 54:588-597, 2015

PubMed Abstract: Carbapenems are the last resort antibiotics for treatment of life-threatening infections. The GES β-lactamases are important contributors to carbapenem resistance in clinical bacterial pathogens. A single amino acid difference at position 170 of the GES-1, GES-2, and GES-5 enzymes is responsible for the expansion of their substrate profile to include carbapenem antibiotics. This highlights the increasing need to understand the mechanisms by which the GES β-lactamases function to aid in development of novel therapeutics. We demonstrate that the catalytic efficiency of the enzymes with carbapenems meropenem, ertapenem, and doripenem progressively increases (100-fold) from GES-1 to -5, mainly due to an increase in the rate of acylation. The data reveal that while acylation is rate limiting for GES-1 and GES-2 for all three carbapenems, acylation and deacylation are indistinguishable for GES-5. The ertapenem-GES-2 crystal structure shows that only the core structure of the antibiotic interacts with the active site of the GES-2 β-lactamase. The identical core structures of ertapenem, doripenem, and meropenem are likely responsible for the observed similarities in the kinetics with these carbapenems. The lack of a methyl group in the core structure of imipenem may provide a structural rationale for the increase in turnover of this carbapenem by the GES β-lactamases. Our data also show that in GES-2 an extensive hydrogen-bonding network between the acyl-enzyme complex and the active site water attenuates activation of this water molecule, which results in poor deacylation by this enzyme.

PubMed: 25485972
DOI: 10.1021/bi501052t

Experimental method

X-RAY DIFFRACTION (1.402 Å)