4RL2

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.008 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.146 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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
  • Primary Citation of Related Structures:  4RL0, 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 ...

    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-1
A, B
246Klebsiella pneumoniaeGene Names: blaNDM-1
EC: 3.5.2.6
Find proteins for C7C422 (Klebsiella pneumoniae)
Go to UniProtKB:  C7C422
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
3S3
Query on 3S3

Download SDF File 
Download CCD File 
A, B
(1R)-2-({(R)-carboxy[(2R,5S)-4-carboxy-5-methyl-5,6-dihydro-2H-1,3-thiazin-2-yl]methyl}amino)-2-oxo-1-phenylethanaminium
C16 H20 N3 O5 S
IEICSSILTYFRBD-QLXFMQRKSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.008 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.146 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 38.620α = 90.00
b = 77.570β = 90.00
c = 132.310γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASESphasing
CrystalCleardata collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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