Pseudomonas aeruginosa Seryl-tRNA Synthetase in Complex with 5'-O-(N-(L-seryl)-sulfamoyl)N3-methyluridine

Experimental Data Snapshot

  • Resolution: 2.22 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

Starting Model: experimental
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Structural Insights into the Binding of Natural Pyrimidine-Based Inhibitors of Class II Aminoacyl-tRNA Synthetases.

Pang, L.Nautiyal, M.De Graef, S.Gadakh, B.Zorzini, V.Economou, A.Strelkov, S.V.Van Aerschot, A.Weeks, S.D.

(2020) ACS Chem Biol 15: 407-415

  • DOI: https://doi.org/10.1021/acschembio.9b00887
  • Primary Citation of Related Structures:  
    6HDZ, 6HE1, 6HE3, 6HHV, 6HHW, 6HHX, 6HHY, 6HHZ, 6HI0, 6RLT, 6RLU, 6RLV, 6S30, 6SJC

  • PubMed Abstract: 

    The pyrimidine-containing Trojan horse antibiotics albomycin and a recently discovered cytidine-containing microcin C analog target the class II seryl- and aspartyl-tRNA synthetases (serRS and aspRS), respectively. The active components of these compounds are competitive inhibitors that mimic the aminoacyl-adenylate intermediate. How they effectively substitute for the interactions mediated by the canonical purine group is unknown. Employing nonhydrolyzable aminoacyl-sulfamoyl nucleosides substituting the base with cytosine, uracil, and N3-methyluracil the structure-activity relationship of the natural compounds was evaluated. In vitro using E. coli serRS and aspRS, the best compounds demonstrated IC 50 values in the low nanomolar range, with a clear preference for cytosine or N3-methyluracil over uracil. X-ray crystallographic structures of K. pneumoniae serRS and T. thermophilus aspRS in complex with the compounds showed the contribution of structured waters and residues in the conserved motif-2 loop in defining base preference. Utilizing the N3-methyluracil bound serRS structure, MD simulations of the fully modified albomycin base were performed to identify the interacting network that drives stable association. This analysis pointed to key interactions with a methionine in the motif-2 loop. Interestingly, this residue is mutated to a glycine in a second serRS (serRS2) found in albomycin-producing actinobacteria possessing self-immunity to this antibiotic. A comparative study demonstrated that serRS2 is poorly inhibited by the pyrimidine-containing intermediate analogs, and an equivalent mutation in E. coli serRS significantly decreased the affinity of the cytosine congener. These findings highlight the crucial role of dynamics and solvation of the motif-2 loop in modulating the binding of the natural antibiotics.

  • Organizational Affiliation

    Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences , KU Leuven , Herestraat 49 Box 822 , B-3000 Leuven , Belgium.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine--tRNA ligase
A, B
426Pseudomonas aeruginosaMutation(s): 0 
Gene Names: serSALP65_01227
Find proteins for Q9I0M6 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I0M6 
Go to UniProtKB:  Q9I0M6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I0M6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FZT (Subject of Investigation/LOI)
Query on FZT

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B]
C13 H20 N4 O10 S
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
H [auth B]
I [auth B]
C [auth A],
D [auth A],
E [auth A],
H [auth B],
I [auth B],
J [auth B]
C2 H6 O2
Query on NA

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.22 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.948α = 90
b = 121.841β = 113.83
c = 65.281γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Research Foundation - FlandersBelgiumG077814N
Research Foundation - FlandersBelgiumG0A4616N
Research Foundation - FlandersBelgium1S53516N

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2020-01-08
    Changes: Database references
  • Version 1.2: 2020-01-15
    Changes: Database references
  • Version 1.3: 2020-03-04
    Changes: Database references
  • Version 1.4: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description