5YPM

Crystal structure of NDM-1 bound to hydrolyzed meropenem representing an EI1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The mechanism of NDM-1-catalyzed carbapenem hydrolysis is distinct from that of penicillin or cephalosporin hydrolysis.

Feng, H.Liu, X.Wang, S.Fleming, J.Wang, D.C.Liu, W.

(2017) Nat Commun 8: 2242-2242

  • DOI: 10.1038/s41467-017-02339-w
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • New Delhi metallo-β-lactamases (NDMs), the recent additions to metallo-β-lactamases (MBLs), pose a serious public health threat due to its highly efficient hydrolysis of β-lactam antibiotics and rapid worldwide dissemination. The MBL-hydrolyzing mech ...

    New Delhi metallo-β-lactamases (NDMs), the recent additions to metallo-β-lactamases (MBLs), pose a serious public health threat due to its highly efficient hydrolysis of β-lactam antibiotics and rapid worldwide dissemination. The MBL-hydrolyzing mechanism for carbapenems is less studied than that of penicillins and cephalosporins. Here, we report crystal structures of NDM-1 in complex with hydrolyzed imipenem and meropenem, at resolutions of 1.80-2.32 Å, together with NMR spectra monitoring meropenem hydrolysis. Three enzyme-intermediate/product derivatives, EI 1 , EI 2 , and EP, are trapped in these crystals. Our structural data reveal double-bond tautomerization from Δ 2 to Δ 1 , absence of a bridging water molecule and an exclusive β-diastereomeric product, all suggesting that the hydrolytic intermediates are protonated by a bulky water molecule incoming from the β-face. These results strongly suggest a distinct mechanism of NDM-1-catalyzed carbapenem hydrolysis from that of penicillin or cephalosporin hydrolysis, which may provide a novel rationale for design of mechanism-based inhibitors.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,School of Stomatology and Medicine, Foshan University, Foshan, Guangdong, 528000, China.,Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.,Institute of Immunology, The Third Military Medical University, Chongqing, 400038, China. wei.liu.2005@gmail.com.,Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. dcwang@ibp.ac.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Metallo-beta-lactamase NDM-1
A, B, C, D, E, F, G, H
242Escherichia coliMutation(s): 0 
Gene Names: blaNDM-1 (bla NDM-1)
Find proteins for E5KIY2 (Escherichia coli)
Go to UniProtKB:  E5KIY2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
8YL
Query on 8YL

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Download CCD File 
A, B, C, D, E, F, G, H
(2S,3R)-2-[(2S,3R)-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl-3-methyl-2,3-dihydro-1H-pyrrole-5-carboxylic acid
Meropenem, hydrolyzed form
C17 H27 N3 O6 S
ILVWWUFTACAPIZ-PQTSNVLCSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B, C, D, E, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 69.790α = 90.00
b = 74.020β = 90.44
c = 155.040γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-02-21
    Type: Initial release