5ZGW

Crystal structure of NDM-1 at pH7.5 with 1 molecule per asymmetric unit (crystallized at succinate pH5.5 and soaked at succinate pH7.5)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.129 

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.


    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
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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
OH
Query on OH

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.129 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.456α = 90.00
b = 59.905β = 98.14
c = 41.740γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-03-10 
  • Released Date: 2018-08-22 
  • Deposition Author(s): Zhang, H., Hao, Q.

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