8I04

Crystal structure of serine acetyltransferase from Salmonella typhimurium complexed with serine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

Starting Model: experimental
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Literature

Alkyl gallates inhibit serine O -acetyltransferase in bacteria and enhance susceptibility of drug-resistant Gram-negative bacteria to antibiotics.

Toyomoto, T.Ono, K.Shiba, T.Momitani, K.Zhang, T.Tsutsuki, H.Ishikawa, T.Hoso, K.Hamada, K.Rahman, A.Wen, L.Maeda, Y.Yamamoto, K.Matsuoka, M.Hanaoka, K.Niidome, T.Akaike, T.Sawa, T.

(2023) Front Microbiol 14: 1276447-1276447

  • DOI: https://doi.org/10.3389/fmicb.2023.1276447
  • Primary Citation of Related Structures:  
    8I04, 8I06, 8I09

  • PubMed Abstract: 

    A principal concept in developing antibacterial agents with selective toxicity is blocking metabolic pathways that are critical for bacterial growth but that mammalian cells lack. Serine O -acetyltransferase (CysE) is an enzyme in many bacteria that catalyzes the first step in l-cysteine biosynthesis by transferring an acetyl group from acetyl coenzyme A (acetyl-CoA) to l-serine to form O -acetylserine. Because mammalian cells lack this l-cysteine biosynthesis pathway, developing an inhibitor of CysE has been thought to be a way to establish a new class of antibacterial agents. Here, we demonstrated that alkyl gallates such as octyl gallate (OGA) could act as potent CysE inhibitors in vitro and in bacteria. Mass spectrometry analyses indicated that OGA treatment markedly reduced intrabacterial levels of l-cysteine and its metabolites including glutathione and glutathione persulfide in Escherichia coli to a level similar to that found in E. coli lacking the cysE gene. Consistent with the reduction of those antioxidant molecules in bacteria, E. coli became vulnerable to hydrogen peroxide-mediated bacterial killing in the presence of OGA. More important, OGA treatment intensified susceptibilities of metallo-β-lactamase-expressing Gram-negative bacteria ( E. coli and Klebsiella pneumoniae ) to carbapenem. Structural analyses showed that alkyl gallate bound to the binding site for acetyl-CoA that limits access of acetyl-CoA to the active site. Our data thus suggest that CysE inhibitors may be used to treat infectious diseases caused by drug-resistant Gram-negative bacteria not only via direct antibacterial activity but also by enhancing therapeutic potentials of existing antibiotics.


  • Organizational Affiliation

    Department of Microbiology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine acetyltransferase
A, B, C
280Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: cysE
EC: 2.3.1.30
UniProt
Find proteins for A0A0D6I3Y9 (Salmonella typhimurium)
Explore A0A0D6I3Y9 
Go to UniProtKB:  A0A0D6I3Y9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0D6I3Y9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.157α = 90
b = 122.157β = 90
c = 128.184γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-22
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Database references