6FOX

The crystal structure of P.fluorescens Kynurenine 3-monooxygenase (KMO) in complex with kynurenine

  • Classification: OXIDOREDUCTASE
  • Organism(s): Pseudomonas fluorescens
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2018-02-08 Released: 2019-08-21 
  • Deposition Author(s): Levy, C.W., Leys, D.
  • Funding Organization(s): Biotechnology and Biological Sciences Research Council, Engineering and Physical Sciences Research Council, Medical Research Council (United Kingdom)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A brain-permeable inhibitor of the neurodegenerative disease target kynurenine 3-monooxygenase prevents accumulation of neurotoxic metabolites.

Zhang, S.Sakuma, M.Deora, G.S.Levy, C.W.Klausing, A.Breda, C.Read, K.D.Edlin, C.D.Ross, B.P.Wright Muelas, M.Day, P.J.O'Hagan, S.Kell, D.B.Schwarcz, R.Leys, D.Heyes, D.J.Giorgini, F.Scrutton, N.S.

(2019) Commun Biol 2: 271-271

  • DOI: 10.1038/s42003-019-0520-5
  • Primary Citation of Related Structures:  
    6FOX, 6FOZ, 6FOY, 6FP1, 6FP0, 6FPH

  • PubMed Abstract: 
  • Dysregulation of the kynurenine pathway (KP) leads to imbalances in neuroactive metabolites associated with the pathogenesis of several neurodegenerative disorders, including Huntington's disease (HD). Inhibition of the enzyme kynurenine 3-monooxygenase (KMO) in the KP normalises these metabolic imbalances and ameliorates neurodegeneration and related phenotypes in several neurodegenerative disease models ...

    Dysregulation of the kynurenine pathway (KP) leads to imbalances in neuroactive metabolites associated with the pathogenesis of several neurodegenerative disorders, including Huntington's disease (HD). Inhibition of the enzyme kynurenine 3-monooxygenase (KMO) in the KP normalises these metabolic imbalances and ameliorates neurodegeneration and related phenotypes in several neurodegenerative disease models. KMO is thus a promising candidate drug target for these disorders, but known inhibitors are not brain permeable. Here, 19 new KMO inhibitors have been identified. One of these ( 1 ) is neuroprotective in a Drosophila HD model but is minimally brain penetrant in mice. The prodrug variant ( 1b ) crosses the blood-brain barrier, releases 1 in the brain, thereby lowering levels of 3-hydroxykynurenine, a toxic KP metabolite linked to neurodegeneration. Prodrug 1b will advance development of targeted therapies against multiple neurodegenerative and neuroinflammatory diseases in which KP likely plays a role, including HD, Alzheimer's disease, and Parkinson's disease.


    Related Citations: 
    • Towards automated crystallographic structure refinement with phenix.refine.
      Afonine, P.V., Grosse-Kunstleve, R.W., Echols, N., Headd, J.J., Moriarty, N.W., Mustyakimov, M., Terwilliger, T.C., Urzhumtsev, A., Zwart, P.H., Adams, P.D.
      (2012) Acta Crystallogr D Biol Crystallogr 68: 352
    • PHENIX: a comprehensive Python-based system for macromolecular structure solution.
      Adams, P.D., Afonine, P.V., Bunkoczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.W., Kapral, G.J., Grosse-Kunstleve, R.W., McCoy, A.J., Moriarty, N.W., Oeffner, R., Read, R.J., Richardson, D.C., Richardson, J.S., Terwilliger, T.C., Zwart, P.H.
      (2010) Acta Crystallogr D Biol Crystallogr 66: 213

    Organizational Affiliation

    1Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, M1 7DN UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Kynurenine 3-monooxygenaseA, B460Pseudomonas fluorescensMutation(s): 1 
Gene Names: kmoqbsG
EC: 1.14.13.9
UniProt
Find proteins for Q84HF5 (Pseudomonas fluorescens)
Explore Q84HF5 
Go to UniProtKB:  Q84HF5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A], F [auth B]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
KYN (Subject of Investigation/LOI)
Query on KYN

Download Ideal Coordinates CCD File 
E [auth B](2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid
C10 H12 N2 O3
YGPSJZOEDVAXAB-QMMMGPOBSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.908α = 90
b = 52.542β = 104.142
c = 136.173γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-02-08 
  • Released Date: 2019-08-21 
  • Deposition Author(s): Levy, C.W., Leys, D.

Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/P009042/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/R000093/1
Engineering and Physical Sciences Research CouncilUnited KingdomEP/J020192/1
Medical Research Council (United Kingdom)United KingdomMR/N00373X/1

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-21
    Type: Initial release
  • Version 1.1: 2020-03-04
    Changes: Database references