NpsA-ThdA, an artificially fused Adenylation-PCP di-domain NRPS from Klebsiella oxytoca

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Biosynthesis, Mechanism of Action, and Inhibition of the Enterotoxin Tilimycin Produced by the Opportunistic PathogenKlebsiella oxytoca.

Alexander, E.M.Kreitler, D.F.Guidolin, V.Hurben, A.K.Drake, E.Villalta, P.W.Balbo, S.Gulick, A.M.Aldrich, C.C.

(2020) ACS Infect Dis 6: 1976-1997

  • DOI: https://doi.org/10.1021/acsinfecdis.0c00326
  • Primary Citation of Related Structures:  
    6VHT, 6VHU, 6VHV, 6VHW, 6VHX, 6VHY, 6VHZ

  • PubMed Abstract: 

    Tilimycin is an enterotoxin produced by the opportunistic pathogen Klebsiella oxytoca that causes antibiotic-associated hemorrhagic colitis (AAHC). This pyrrolobenzodiazepine (PBD) natural product is synthesized by a bimodular nonribosomal peptide synthetase (NRPS) pathway composed of three proteins: NpsA, ThdA, and NpsB. We describe the functional and structural characterization of the fully reconstituted NRPS system and report the steady-state kinetic analysis of all natural substrates and cofactors as well as the structural characterization of both NpsA and ThdA. The mechanism of action of tilimycin was confirmed using DNA adductomics techniques through the detection of putative N-2 guanine alkylation after tilimycin exposure to eukaryotic cells, providing the first structural characterization of a PBD-DNA adduct formed in cells. Finally, we report the rational design of small-molecule inhibitors that block tilimycin biosynthesis in whole cell K. oxytoca (IC 50 = 29 ± 4 μM) through the inhibition of NpsA ( K D = 29 ± 4 nM).

  • Organizational Affiliation

    Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NpsA Adenylation Domain, Non-ribosomal peptide synthetase fusion protein
A, B, C, D
586Klebsiella oxytocaMutation(s): 4 
Gene Names: AGF18_11095AGF18_11090
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QXD (Subject of Investigation/LOI)
Query on QXD

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth C],
H [auth D]
C29 H43 N8 O13 P S2
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.54α = 95.331
b = 98.721β = 96.337
c = 118.754γ = 106.508
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
autoPROCdata scaling
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM116957

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-24
    Type: Initial release
  • Version 1.1: 2020-07-22
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description