6K4T

Crystal structure of SMB-1 metallo-beta-lactamase in a complex with TSA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

4-Amino-2-Sulfanylbenzoic Acid as a Potent Subclass B3 Metallo-beta-Lactamase-Specific Inhibitor Applicable for Distinguishing Metallo-beta-Lactamase Subclasses.

Wachino, J.Kanechi, R.Nishino, E.Mochizuki, M.Jin, W.Kimura, K.Kurosaki, H.Arakawa, Y.

(2019) Antimicrob Agents Chemother 63

  • DOI: 10.1128/AAC.01197-19
  • Primary Citation of Related Structures:  
    5Y5B, 6JED, 6K4X, 6K4T

  • PubMed Abstract: 
  • The number of cases of infection with carbapenem-resistant Enterobacteriaceae (CRE) has been increasing and has become a major clinical and public health concern. Production of metallo-β-lactamases (MBLs) is one of the principal carbapenem r ...

    The number of cases of infection with carbapenem-resistant Enterobacteriaceae (CRE) has been increasing and has become a major clinical and public health concern. Production of metallo-β-lactamases (MBLs) is one of the principal carbapenem resistance mechanisms in CRE. Therefore, developing MBL inhibitors is a promising strategy to overcome the problems of carbapenem resistance conferred by MBLs. To date, the development and evaluation of MBL inhibitors have focused on subclass B1 MBLs but not on B3 MBLs. In the present study, we searched for B3 MBL (specifically, SMB-1) inhibitors and found thiosalicylic acid (TSA) to be a potent inhibitor of B3 SMB-1 MBL (50% inhibitory concentration [IC 50 ], 0.95 μM). TSA inhibited the purified SMB-1 to a considerable degree but was not active against Escherichia coli cells producing SMB-1, as the meropenem (MEM) MIC for the SMB-1 producer was only slightly reduced with TSA. We then introduced a primary amine to TSA and synthesized 4-amino-2-sulfanylbenzoic acid (ASB), which substantially reduced the MEM MICs for SMB-1 producers. X-ray crystallographic analyses revealed that ASB binds to the two zinc ions, Ser221, and Thr223 at the active site of SMB-1. These are ubiquitously conserved residues across clinically relevant B3 MBLs. ASB also significantly inhibited other B3 MBLs, including AIM-1, LMB-1, and L1. Therefore, the characterization of ASB provides a starting point for the development of optimum B3 MBL inhibitors.


    Organizational Affiliation

    Department of Bacteriology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Metallo-beta-lactamaseA262Serratia marcescensMutation(s): 0 
Gene Names: SMB-1
EC: 3.5.2.6
Find proteins for G5ELM3 (Serratia marcescens)
Explore G5ELM3 
Go to UniProtKB:  G5ELM3
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JKE
Query on JKE

Download CCD File 
A
2-sulfanylbenzoic acid
C7 H6 O2 S
NBOMNTLFRHMDEZ-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.04α = 108.6
b = 41.59β = 102.75
c = 45.55γ = 106.06
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2019-05-27 
  • Released Date: 2019-08-07 
  • Deposition Author(s): Wachino, J.

Revision History 

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Database references