5Y5B | pdb_00005y5b

Crystal Structure Of IMP-1 Metallo-beta-lactamase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.199 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.155 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 
    0.157 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 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: https://doi.org/10.1128/AAC.01197-19
  • Primary Citation Related Structures: 
    5Y5B, 6JED, 6K4T, 6K4X

  • 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 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 wachino@med.nagoya-u.ac.jp.

Macromolecule Content 

  • Total Structure Weight: 25.85 kDa 
  • Atom Count: 2,028 
  • Modeled Residue Count: 221 
  • Deposited Residue Count: 228 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Metallo-beta-lactamase type 2228Serratia marcescensMutation(s): 0 
EC: 3.5.2.6 (PDB Primary Data), 3.1.26 (UniProt)
UniProt
Find proteins for P52699 (Serratia marcescens)
Explore P52699 
Go to UniProtKB:  P52699
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52699
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.199 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.155 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 0.157 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.01α = 90
b = 57.73β = 90
c = 101.06γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2018-08-08 
  • Deposition Author(s): Wachino, J.

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description