4RL0

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.132 

wwPDB Validation 3D Report Full Report



Literature

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: 10.1021/ja508388e
  • Structures With Same Primary Citation

  • 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 ...

    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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase NDM-1A, B242Klebsiella pneumoniaeMutation(s): 0 
Gene Names: blaNDM-1
EC: 3.5.2.6
Find proteins for C7C422 (Klebsiella pneumoniae)
Explore C7C422 
Go to UniProtKB:  C7C422
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3S0
Query on 3S0

Download CCD File 
A, B
(2R,5S)-5-[(carbamoyloxy)methyl]-2-[(R)-carboxy{[(2Z)-2-(furan-2-yl)-2-(methoxyimino)acetyl]amino}methyl]-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
C16 H18 N4 O9 S
AYUIRPIPSPPXAA-NEHUYCMOSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.132 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.18α = 90
b = 78.89β = 90
c = 133.06γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASESphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-19
    Type: Initial release