ISDA

Deposition Date 2020-01-10

Release Date 2020-06-24

Last Version Date 2023-10-11

Entry Detail

PDB ID:

6VHT

Keywords:

BIOSYNTHETIC PROTEIN

Title:

Klebsiella oxytoca NpsA N-terminal subdomain in space group C2

Biological Source:

Source Organism:

Klebsiella oxytoca (Taxon ID: 571)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.84 Å

R-Value Free:

0.24

R-Value Work:

0.20

R-Value Observed:

0.21

Space Group:

C 1 2 1

Download Validation Report

Macromolecular Entities

Polymer Type:polypeptide(L)
Molecule:NpsA Adenylation Domain
Mutations:E312A, E313A, Q314A
Chain IDs:A
Chain Length:406
Number of Molecules:1
Biological Source:Klebsiella oxytoca

Ligand Molecules

Primary Citation

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.Show

Acs Infect Dis. 6 1976 1997 (2020)

PMID: 32485104 DOI: 10.1021/acsinfecdis.0c00326

Abstact

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 (IC50 = 29 ± 4 μM) through the inhibition of NpsA (KD = 29 ± 4 nM).

Legend

Protein

Chemical

Disease

Primary Citation of related structures