3M2K

Crystal Structure of fluorescein-labeled Class A -beta lactamase PenP in complex with cefotaxime


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.180 

Starting Model: experimental
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This is version 2.2 of the entry. See complete history


Literature

Structural studies of the mechanism for biosensing antibiotics in a fluorescein-labeled beta-lactamase.

Wong, W.T.Au, H.W.Yap, H.K.Leung, Y.C.Wong, K.Y.Zhao, Y.

(2011) BMC Struct Biol 11: 15-15

  • DOI: https://doi.org/10.1186/1472-6807-11-15
  • Primary Citation of Related Structures:  
    3M2K

  • PubMed Abstract: 

    β-lactamase conjugated with environment-sensitive fluorescein molecule to residue 166 on the Ω-loop near its catalytic site is a highly effective biosensor for β-lactam antibiotics. Yet the molecular mechanism of such fluorescence-based biosensing is not well understood. Here we report the crystal structure of a Class A β-lactamase PenP from Bacillus licheniformis 749/C with fluorescein conjugated at residue 166 after E166C mutation, both in apo form (PenP-E166Cf) and in covalent complex form with cefotaxime (PenP-E166Cf-cefotaxime), to illustrate its biosensing mechanism. In the apo structure the fluorescein molecule partially occupies the antibiotic binding site and is highly dynamic. In the PenP-E166Cf-cefatoxime complex structure the binding and subsequent acylation of cefotaxime to PenP displaces fluorescein from its original location to avoid steric clash. Such displacement causes the well-folded Ω-loop to become fully flexible and the conjugated fluorescein molecule to relocate to a more solvent exposed environment, hence enhancing its fluorescence emission. Furthermore, the fully flexible Ω-loop enables the narrow-spectrum PenP enzyme to bind cefotaxime in a mode that resembles the extended-spectrum β-lactamase. Our structural studies indicate the biosensing mechanism of a fluorescein-labelled β-lactamase. Such findings confirm our previous proposal based on molecular modelling and provide useful information for the rational design of β-lactamase-based biosensor to detect the wide spectrum of β-lactam antibiotics. The observation of increased Ω-loop flexibility upon conjugation of fluorophore may have the potential to serve as a screening tool for novel β-lactamase inhibitors that target the Ω-loop and not the active site.


  • Organizational Affiliation

    Department of Applied Biology and Chemical Technology, Central Laboratory of Institute of Molecular Technology for Drug Discovery and Synthesis, The Hong Kong Polytechnic University, Hung Hom, Hong Hong, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase
A, B
257Bacillus licheniformisMutation(s): 1 
Gene Names: penP
EC: 3.5.2.6
UniProt
Find proteins for P00808 (Bacillus licheniformis)
Explore P00808 
Go to UniProtKB:  P00808
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00808
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.538α = 90
b = 91.524β = 104.22
c = 66.302γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-08-24
    Changes: Non-polymer description
  • Version 2.0: 2018-09-19
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.2: 2024-10-09
    Changes: Structure summary