5ZGE

Crystal structure of NDM-1 at pH5.5 (Bis-Tris) in complex with hydrolyzed ampicillin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.128 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Active-Site Conformational Fluctuations Promote the Enzymatic Activity of NDM-1.

Zhang, H.Ma, G.Zhu, Y.Zeng, L.Ahmad, A.Wang, C.Pang, B.Fang, H.Zhao, L.Hao, Q.

(2018) Antimicrob. Agents Chemother. 62: --

  • DOI: 10.1128/AAC.01579-18
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • β-Lactam antibiotics are the mainstay for the treatment of bacterial infections. However, elevated resistance to these antibiotics mediated by metallo-β-lactamases (MBLs) has become a global concern. New Delhi metallo-β-lactamase-1 (NDM-1), a newly a ...

    β-Lactam antibiotics are the mainstay for the treatment of bacterial infections. However, elevated resistance to these antibiotics mediated by metallo-β-lactamases (MBLs) has become a global concern. New Delhi metallo-β-lactamase-1 (NDM-1), a newly added member of the MBL family that can hydrolyze almost all β-lactam antibiotics, has rapidly spread all over the world and poses serious clinical threats. Broad-spectrum and mechanism-based inhibitors against all MBLs are highly desired, but the differential mechanisms of MBLs toward different antibiotics pose a great challenge. To facilitate the design of mechanism-based inhibitors, we investigated the active-site conformational changes of NDM-1 through the determination of a series of 15 high-resolution crystal structures in native form and in complex with products and by using biochemical and biophysical studies, site-directed mutagenesis, and molecular dynamics computation. The structural studies reveal the consistency of the active-site conformations in NDM-1/product complexes and the fluctuation in native NDM-1 structures. The enzymatic measurements indicate a correlation between enzymatic activity and the active-site fluctuation, with more fluctuation favoring higher activity. This correlation is further validated by structural and enzymatic studies of the Q123G mutant. Our combinational studies suggest that active-site conformational fluctuation promotes the enzymatic activity of NDM-1, which may guide further mechanism studies and inhibitor design.


    Related Citations: 
    • Crystal structure of NDM-1 reveals a common beta-lactam hydrolysis mechanism.
      Zhang, H.,Hao, Q.
      (2011) FASEB J. 25: 2574


    Organizational Affiliation

    Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen, China zhanghm@sustc.edu.cn qhao@hku.hk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Metallo-beta-lactamase type 2
A, B
242Klebsiella pneumoniaeMutation(s): 0 
Gene Names: blaNDM-1
EC: 3.5.2.6
Find proteins for C7C422 (Klebsiella pneumoniae)
Go to UniProtKB:  C7C422
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZZ7
Query on ZZ7

Download SDF File 
Download CCD File 
A, B
(2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid
AMPICILLIN (open form)
C16 H21 N3 O5 S
KDAWOPKDXRJNHV-MPPDQPJWSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A, B
HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.128 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.204α = 90.00
b = 79.071β = 90.00
c = 133.974γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
PDB_EXTRACTdata extraction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-03-08 
  • Released Date: 2018-08-22 
  • Deposition Author(s): Zhang, H., Hao, Q.
  • This entry supersedes: 3Q6X

Funding OrganizationLocationGrant Number
National Science Foundation (China)China31670753

Revision History 

  • Version 1.0: 2018-08-22
    Type: Initial release
  • Version 1.1: 2018-09-19
    Type: Data collection, Database references
  • Version 1.2: 2018-12-12
    Type: Data collection, Database references