9JSE | pdb_00009jse

Crystal Structure of PenI beta-Lactamase from Burkholderia pseudomallei Complex with Taniborbactam


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 
    0.151 (Depositor), 0.149 (DCC) 
  • R-Value Work: 
    0.125 (Depositor), 0.125 (DCC) 
  • R-Value Observed: 
    0.126 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

Burkholderia pseudomallei PenI beta-lactamase and variants are potently inhibited by taniborbactam.

Mojica, M.F.Becka, S.A.Edwards, M.Myers, C.Uehara, K.Uehara, T.Hoshino, T.Zeiser, E.T.Chatwin, C.L.Six, D.A.Bonomo, R.A.Papp-Wallace, K.M.Nukaga, M.

(2025) Antimicrob Agents Chemother 69: e0078725-e0078725

  • DOI: https://doi.org/10.1128/aac.00787-25
  • Primary Citation Related Structures: 
    9JSE

  • PubMed Abstract: 

    Burkholderia pseudomallei is a Gram-negative pathogen that causes melioidosis, a severe and often fatal disease. Due to its recognized potential as a bioterrorism agent, it is critical that appropriate antimicrobial agents are available for post-exposure prophylaxis and treatment of melioidosis. Cefepime-taniborbactam is a novel β-lactam-β-lactamase inhibitor combination in clinical development, with promising activity against Gram-negative bacteria producing class A, B, C, and/or D β-lactamases. Herein, we demonstrate the inhibitory activity of taniborbactam against PenI, the class A β-lactamase produced by B. pseudomallei . Isogenic Escherichia coli strains producing PenI and its ceftazidime-resistance-conferring variants (C69Y and P167S) showed ceftazidime minimum inhibitory concentration (MIC) of 64 mg/L for the strain producing PenI and 1,024 mg/L for the strains producing the variants, whereas cefepime MIC was 128-256 mg/L for these three strains. While the addition of avibactam decreased ceftazidime MIC to 1 mg/L for PenI and 8-16 mg/L for the variants, the addition of taniborbactam decreased cefepime MIC to ≤0.5 mg/L for PenI and the variants. Similarly, an 8-fold reduction of the cefepime MIC upon addition of taniborbactam was observed in an avirulent B. pseudomallei strain. Furthermore, taniborbactam inhibited PenI and its C69Y variant with an apparent K i of 0.11 and 3.1 µM, respectively. Lastly, co-crystallography and molecular dynamics simulations showed that taniborbactam induced the formation of a disulfide bond between Cys77 and Cys123, which destabilizes the deacylation water and strengthens the taniborbactam-PenI complex. These results support the development of cefepime-taniborbactam as a promising agent for the treatment of infections by B. pseudomallei .


  • Organizational Affiliation
    • Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.

Macromolecule Content 

  • Total Structure Weight: 28.6 kDa 
  • Atom Count: 2,348 
  • Modeled Residue Count: 264 
  • Deposited Residue Count: 264 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-lactamase264Burkholderia pseudomallei K96243Mutation(s): 0 
Gene Names: penAblaABPSS0946
EC: 3.5.2.6
UniProt
Find proteins for H7C785 (Burkholderia pseudomallei (strain K96243))
Explore H7C785 
Go to UniProtKB:  H7C785
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH7C785
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KJK
(Subject of Investigation/LOI)

Query on KJK



Download:Ideal Coordinates CCD File
B [auth A](3~{R})-3-[2-[4-(2-azanylethylamino)cyclohexyl]ethanoylamino]-2-oxidanyl-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic acid
C19 H28 B N3 O5
PFZUWUXKQPRWAL-NOLJZWGESA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free:  0.151 (Depositor), 0.149 (DCC) 
  • R-Value Work:  0.125 (Depositor), 0.125 (DCC) 
  • R-Value Observed: 0.126 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.202α = 90
b = 52.12β = 92.554
c = 50.436γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201300019C
Wellcome TrustUnited Kingdom360G-Wellcome-101999/Z/13/Z
Department of Health & Human Services (HHS)United StatesHHSO100201900007C
Department of Veterans Affairs (VA, United States)United StatesBX002872

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-13
    Type: Initial release
  • Version 1.1: 2025-09-24
    Changes: Database references
  • Version 1.2: 2025-10-15
    Changes: Database references