6VHY | pdb_00006vhy

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

• PDB DOI: https://doi.org/10.2210/pdb6VHY/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Klebsiella oxytoca
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-01-10 Released: 2020-06-24 
• Deposition Author(s): Kreitler, D.F., Gulick, A.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.260 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

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

• PubMed: 32485104 
• DOI: https://doi.org/10.1021/acsinfecdis.0c00326
• Primary Citation 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).

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Organizational Affiliation: 
• Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States.
Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203, United States.
Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States.
Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, Minnesota 55455, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 259.48 kDa 
• Atom Count: 15,436 
• Modeled Residue Count: 2,093 
• Deposited Residue Count: 2,344 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NpsA Adenylation Domain, Non-ribosomal peptide synthetase fusion protein	A, B, C, D	586	Klebsiella oxytoca	Mutation(s): 4  Gene Names: AGF18_11095, AGF18_11090

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QXD (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	5'-deoxy-5'-({[(2R)-2-{[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}-2-(3-hydroxyphenyl)ethyl]sulfonyl}amino)adenosine C29 H43 N8 O13 P S2 ADMPPCCGBBJHMD-XCYBABBZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.260 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.54	α = 95.331
b = 98.721	β = 96.337
c = 118.754	γ = 106.508

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
autoPROC	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-06-24 
Deposition Author(s): Kreitler, D.F., Gulick, A.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM116957

Revision History  

• 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
• Version 1.3: 2024-11-20
  Changes: Structure summary