6VHW

Klebsiella oxytoca NpsA N-terminal subdomain in complex with 3-hydroxybenzoyl-AMSN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

wwPDB Validation 3D Report Full Report



Literature

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

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

(2020) ACS Infect Dis 

  • DOI: 10.1021/acsinfecdis.0c00326
  • Structures With Same Primary Citation

  • 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 sy ...

    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 comprised 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).


    Organizational Affiliation

    School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NpsA Adenylation Domain
A, B
406Klebsiella oxytocaMutation(s): 4 
Gene Names: NPSAAGF18_11095
Find proteins for A0A2U4DY99 (Klebsiella oxytoca)
Go to UniProtKB:  A0A2U4DY99
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
R2V
Query on R2V

Download CCD File 
A, B
5'-deoxy-5'-{[(3-hydroxybenzene-1-carbonyl)sulfamoyl]amino}adenosine
C17 H19 N7 O7 S
DNCWBHYPLQFCLB-CNEMSGBDSA-N
 Ligand Interaction
EPE
Query on EPE

Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download CCD File 
A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
BR
Query on BR

Download CCD File 
A, B
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.436α = 90
b = 60.284β = 101.009
c = 80.253γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
AutoPROCdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



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 

  • Version 1.0: 2020-06-24
    Type: Initial release