6VHZ | pdb_00006vhz

Klebsiella oxytoca NpsA N-terminal subdomain in complex with anthranilyl-AMSN

PDB DOI: https://doi.org/10.2210/pdb6VHZ/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Klebsiella oxytoca 10-5243
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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free:
0.227 (Depositor), 0.233 (DCC)
R-Value Work:
0.203 (Depositor), 0.208 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
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).

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 89.19 kDa
Atom Count: 5,769
Modeled Residue Count: 764
Deposited Residue Count: 812
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NpsA Adenylation Domain	A, B	406	Klebsiella oxytoca 10-5243	Mutation(s): 4 Gene Names: NPSA

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QXP (Subject of Investigation/LOI) Query on QXP Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B]	5'-{[(benzenecarbonyl)sulfamoyl]amino}-5'-deoxyadenosine C₁₇ H₂₀ N₈ O₆ S VRCFLQCMFIZPPZ-CNEMSGBDSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
BR Query on BR Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B]	J [auth B], K [auth B]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain J [auth B] Focus chain K [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.227 (Depositor), 0.233 (DCC)
R-Value Work: 0.203 (Depositor), 0.208 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.013	α = 90
b = 61.408	β = 100.434
c = 80.518	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-06-24

Deposition Author(s):

Kreitler, D.F.

Gulick, A.M.

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

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