9ENX | pdb_00009enx

Enmetazobactam-Derived GES-1 Acyl-Enzyme

• PDB DOI: https://doi.org/10.2210/pdb9ENX/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-03-13 Released: 2025-03-26 
• Deposition Author(s): Beer, M., Hinchliffe, P., Spencer, J.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.23 Å
• R-Value Free: 
  0.194 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.151 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

Mechanistic basis for inhibition of the extended-spectrum beta-lactamase GES-1 by enmetazobactam and tazobactam.

Beer, M., Hinchliffe, P., Hanzevacki, M., Bethel, C.R., Tooke, C.L., Van der Kamp, M.W., Papp-Wallace, K.M., Bonomo, R.A., Shapiro, S., Mulholland, A.J., Spencer, J.

(2025) FEBS Lett 599: 3284-3300

• PubMed: 40944392 
• DOI: https://doi.org/10.1002/1873-3468.70155
• Primary Citation Related Structures: 
  9ENV, 9ENW, 9ENX, 9ENY


• PubMed Abstract: 
  

  β-Lactamase-catalysed hydrolysis is the primary form of β-lactam antibiotic resistance in Gram-negative bacteria. The penicillanic acid sulfone (PAS) enmetazobactam is thought to inhibit extended-spectrum β-lactamases (ESBLs) by fragmentation of an initial acyl-enzyme to form an active-site lysinoalanine cross link. We investigate interactions of enmetazobactam and its congener tazobactam with GES-1, an ESBL with structural features of carbapenem-hydrolysing β-lactamases. Crystal structures show different breakdown products of the two inhibitors covalently bound to the catalytic Ser70, assigned using quantum mechanics/molecular mechanics (QM/MM) calculations. We find no evidence for lysinoalanine formation, with mass spectrometry indicating active enzyme regeneration, behaviour previously observed for carbapenem-hydrolysing enzymes, but not ESBLs. This work establishes that PAS inhibitors interact with diverse β-lactamases by differing mechanisms, which should inform development of future compounds.

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Organizational Affiliation: 
• School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK.
Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK.
Research Service, Louis Stokes Cleveland Department of Veterans Affairs, Cleveland, OH, USA.
Department of Biology and Biochemistry, 4 South, University of Bath, Bath, UK.
School of Biochemistry, University of Bristol, Bristol, UK.
Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, USA.
Department of Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
Harry Lime Institute for Penicillin Research, Basel, Switzerland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 64.44 kDa 
• Atom Count: 4,818 
• Modeled Residue Count: 530 
• Deposited Residue Count: 578 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-lactamase	A, B	289	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: ges-1, blaGES-1 EC: 3.5.2.6
UniProt
Find proteins for Q09HD0 (Klebsiella pneumoniae) Explore Q09HD0  Go to UniProtKB:  Q09HD0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
M9W (Subject of Investigation/LOI)	G [auth A], I [auth B]	Enmetazobactam derived trans-enamine adduct C11 H17 N4 O6 S VVXNTAXAJHAELU-UEVFTQGLSA-O
EPE	C [auth A], H [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
MPD	D [auth A], E [auth A], F [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.23 Å
• R-Value Free:  0.194 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.151 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.804	α = 90
b = 81.034	β = 101.81
c = 71.551	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-03-26 
Deposition Author(s): Beer, M., Hinchliffe, P., Spencer, J.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/T008741/10

Revision History  

• Version 1.0: 2025-03-26
  Type: Initial release
  
• Version 1.1: 2026-10-28
  Changes: Database references