8PCC

Structure of serine-beta-lactamase CTX-M-14 following the time-resolved active site binding of boric acid, 100 ms


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

Time-resolved crystallography of boric acid binding to the active site serine of the beta-lactamase CTX-M-14 and subsequent 1,2-diol esterification.

Prester, A.Perbandt, M.Galchenkova, M.Oberthuer, D.Werner, N.Henkel, A.Maracke, J.Yefanov, O.Hakanpaa, J.Pompidor, G.Meyer, J.Chapman, H.Aepfelbacher, M.Hinrichs, W.Rohde, H.Betzel, C.

(2024) Commun Chem 7: 152-152

  • DOI: https://doi.org/10.1038/s42004-024-01236-w
  • Primary Citation of Related Structures:  
    8PC9, 8PCA, 8PCB, 8PCC, 8PCD, 8PCE, 8PCF, 8PCG, 8PCI, 8PCJ, 8PCK, 8PCL, 8PCM, 8PCN, 8PCO, 8PCP, 8PCQ, 8PCR, 8PCS, 8PCT, 8PCU, 8PCV, 8R7M

  • PubMed Abstract: 

    The emergence and spread of antibiotic resistance represent a growing threat to public health. Of particular concern is the appearance of β-lactamases, which are capable to hydrolyze and inactivate the most important class of antibiotics, the β-lactams. Effective β-lactamase inhibitors and mechanistic insights into their action are central in overcoming this type of resistance, and in this context boronate-based β-lactamase inhibitors were just recently approved to treat multidrug-resistant bacteria. Using boric acid as a simplified inhibitor model, time-resolved serial crystallography was employed to obtain mechanistic insights into binding to the active site serine of β-lactamase CTX-M-14, identifying a reaction time frame of 80-100 ms. In a next step, the subsequent 1,2-diol boric ester formation with glycerol in the active site was monitored proceeding in a time frame of 100-150 ms. Furthermore, the displacement of the crucial anion in the active site of the β-lactamase was verified as an essential part of the binding mechanism of substrates and inhibitors. In total, 22 datasets of β-lactamase intermediate complexes with high spatial resolution of 1.40-2.04 Å and high temporal resolution range of 50-10,000 ms were obtained, allowing a detailed analysis of the studied processes. Mechanistic details captured here contribute to the understanding of molecular processes and their time frames in enzymatic reactions. Moreover, we could demonstrate that time-resolved crystallography can serve as an additional tool for identifying and investigating enzymatic reactions.


  • Organizational Affiliation

    Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf UKE, Hamburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase263Klebsiella pneumoniaeMutation(s): 0 
EC: 3.5.2.6
UniProt
Find proteins for A0A0H3H219 (Klebsiella pneumoniae subsp. pneumoniae (strain HS11286))
Explore A0A0H3H219 
Go to UniProtKB:  A0A0H3H219
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3H219
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.84α = 90
b = 41.84β = 90
c = 233.28γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted BO4Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Joachim Herz StiftungGermany--
German Federal Ministry for Education and ResearchGermany--
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-26
    Type: Initial release
  • Version 1.1: 2024-07-17
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Structure summary