5YPK

Crystal structure of NDM-1 bound to hydrolyzed imipenem representing an EI2 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1038/s41467-017-02339-w
  • Primary Citation of Related Structures:  
    5YPI, 5YPK, 5YPL, 5YPM, 5YPN

  • 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 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Metallo-beta-lactamase NDM-1
A, B, C, D, E
A, B, C, D, E, F, G, H
242Escherichia coliMutation(s): 0 
Gene Names: blaNDM-1
EC: 3.5.2.6
UniProt
Find proteins for E5KIY2 (Escherichia coli)
Explore E5KIY2 
Go to UniProtKB:  E5KIY2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE5KIY2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HIW (Subject of Investigation/LOI)
Query on HIW

Download Ideal Coordinates CCD File 
GA [auth E]
K [auth A]
LA [auth F]
O [auth B]
QA [auth G]
GA [auth E],
K [auth A],
LA [auth F],
O [auth B],
QA [auth G],
S [auth C],
UA [auth H],
Z [auth D]
(2R,4S)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-4-[(2-{[(Z)-iminomethyl]amino}ethyl)sulfanyl]-3,4-dihydro-2H-pyrrole-5-ca rboxylic acid
C12 H19 N3 O5 S
GGEWNUMDSNUHAH-LURQLKTLSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth D]
HA [auth E]
L [auth A]
MA [auth F]
P [auth B]
AA [auth D],
HA [auth E],
L [auth A],
MA [auth F],
P [auth B],
T [auth C],
U [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

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EA [auth E]
FA [auth E]
I [auth A]
J [auth A]
JA [auth F]
EA [auth E],
FA [auth E],
I [auth A],
J [auth A],
JA [auth F],
KA [auth F],
M [auth B],
N [auth B],
OA [auth G],
PA [auth G],
Q [auth C],
R [auth C],
SA [auth H],
TA [auth H],
X [auth D],
Y [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

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BA [auth D]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

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CA [auth D]
DA [auth D]
IA [auth E]
NA [auth F]
RA [auth G]
CA [auth D],
DA [auth D],
IA [auth E],
NA [auth F],
RA [auth G],
V [auth C],
W [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.24α = 90
b = 73.61β = 90.08
c = 154.52γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-21
    Type: Initial release
  • Version 1.1: 2018-05-16
    Changes: Data collection
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary