Structural and mechanistic insights into NDM-1 catalyzed hydrolysis of cephalosporins

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 

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Structural and Mechanistic Insights into NDM-1 Catalyzed Hydrolysis of Cephalosporins.

Feng, H.Ding, J.Zhu, D.Liu, X.Xu, X.Zhang, Y.Zang, S.Wang, D.C.Liu, W.

(2014) J Am Chem Soc 136: 14694-14697

  • DOI: https://doi.org/10.1021/ja508388e
  • Primary Citation of Related Structures:  
    4RL0, 4RL2, 4RM5

  • PubMed Abstract: 

    Cephalosporins constitute a large class of β-lactam antibiotics clinically used as antimicrobial drugs. New Dehli metallo-β-lactamase (NDM-1) poses a global threat to human health as it confers on bacterial pathogen resistance to almost all β-lactams, including penicillins, cephalosporins, and carbapenems. Here we report the first crystal structures of NDM-1 in complex with cefuroxime and cephalexin, as well as NMR spectra monitoring cefuroxime and cefixime hydrolysis catalyzed by NDM-1. Surprisingly, cephalosporoate intermediates were captured in both crystal structures determined at 1.3 and 2.0 Å. These results provide detailed information concerning the mechanism and pathways of cephalosporin hydrolysis. We also present the crystal structure and enzyme assays of a D124N mutant, which reveals that D124 most likely plays a more structural than catalytic role.

  • Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase NDM-1
A, B, C, D
242Klebsiella pneumoniaeMutation(s): 1 
Gene Names: blaNDM-1
Find proteins for C7C422 (Klebsiella pneumoniae)
Explore C7C422 
Go to UniProtKB:  C7C422
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC7C422
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.1α = 87.62
b = 68.12β = 88.34
c = 68.91γ = 77.42
Software Package:
Software NamePurpose
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-19
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description