6YK0

Crystal structure of mouse pyridoxal kinase in complex with ATP-gamma-S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Pyridoxal kinase inhibition by artemisinins down-regulates inhibitory neurotransmission.

Kasaragod, V.B.Pacios-Michelena, A.Schaefer, N.Zheng, F.Bader, N.Alzheimer, C.Villmann, C.Schindelin, H.

(2020) Proc Natl Acad Sci U S A 117: 33235-33245

  • DOI: https://doi.org/10.1073/pnas.2008695117
  • Primary Citation of Related Structures:  
    6YJZ, 6YK0, 6YK1

  • PubMed Abstract: 

    The antimalarial artemisinins have also been implicated in the regulation of various cellular pathways including immunomodulation of cancers and regulation of pancreatic cell signaling in mammals. Despite their widespread application, the cellular specificities and molecular mechanisms of target recognition by artemisinins remain poorly characterized. We recently demonstrated how these drugs modulate inhibitory postsynaptic signaling by direct binding to the postsynaptic scaffolding protein gephyrin. Here, we report the crystal structure of the central metabolic enzyme pyridoxal kinase (PDXK), which catalyzes the production of the active form of vitamin B6 (also known as pyridoxal 5'-phosphate [PLP]), in complex with artesunate at 2.4-Å resolution. Partially overlapping binding of artemisinins with the substrate pyridoxal inhibits PLP biosynthesis as demonstrated by kinetic measurements. Electrophysiological recordings from hippocampal slices and activity measurements of glutamic acid decarboxylase (GAD), a PLP-dependent enzyme synthesizing the neurotransmitter γ-aminobutyric acid (GABA), define how artemisinins also interfere presynaptically with GABAergic signaling. Our data provide a comprehensive picture of artemisinin-induced effects on inhibitory signaling in the brain.


  • Organizational Affiliation

    Institute of Structural Biology, Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Würzburg, Germany; vkasaragod@mrc-lmb.cam.ac.uk hermann.schindelin@virchow.uni-wuerzburg.de.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyridoxal kinase
A, B, C, D
314Mus musculusMutation(s): 0 
Gene Names: PdxkPkh
EC: 2.7.1.35
UniProt & NIH Common Fund Data Resources
Find proteins for Q8K183 (Mus musculus)
Explore Q8K183 
Go to UniProtKB:  Q8K183
IMPC:  MGI:1351869
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8K183
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGS
Query on AGS

Download Ideal Coordinates CCD File 
CA [auth D],
F [auth A],
L [auth B],
U [auth C]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
PG4 (Subject of Investigation/LOI)
Query on PG4

Download Ideal Coordinates CCD File 
E [auth A],
H [auth A]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A],
N [auth B],
W [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
DA [auth D]
G [auth A]
J [auth A]
AA [auth C],
BA [auth C],
DA [auth D],
G [auth A],
J [auth A],
K [auth A],
M [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
V [auth C],
X [auth C],
Y [auth C],
Z [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 278.6α = 90
b = 53.021β = 91.75
c = 109.851γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySCHI425/8-2

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-14
    Type: Initial release
  • Version 1.1: 2022-04-27
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Refinement description