6OID | pdb_00006oid

Redox Regulation of FN3K from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 
    0.204 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6OID

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

A redox-active switch in fructosamine-3-kinases expands the regulatory repertoire of the protein kinase superfamily.

Shrestha, S.Katiyar, S.Sanz-Rodriguez, C.E.Kemppinen, N.R.Kim, H.W.Kadirvelraj, R.Panagos, C.Keyhaninejad, N.Colonna, M.Chopra, P.Byrne, D.P.Boons, G.J.van der Knaap, E.Eyers, P.A.Edison, A.S.Wood, Z.A.Kannan, N.

(2020) Sci Signal 13

  • DOI: https://doi.org/10.1126/scisignal.aax6313
  • Primary Citation Related Structures: 
    6OID

  • PubMed Abstract: 

    Aberrant regulation of metabolic kinases by altered redox homeostasis substantially contributes to aging and various diseases, such as diabetes. We found that the catalytic activity of a conserved family of fructosamine-3-kinases (FN3Ks), which are evolutionarily related to eukaryotic protein kinases, is regulated by redox-sensitive cysteine residues in the kinase domain. The crystal structure of the FN3K homolog from Arabidopsis thaliana revealed that it forms an unexpected strand-exchange dimer in which the ATP-binding P-loop and adjoining β strands are swapped between two chains in the dimer. This dimeric configuration is characterized by strained interchain disulfide bonds that stabilize the P-loop in an extended conformation. Mutational analysis and solution studies confirmed that the strained disulfides function as redox "switches" to reversibly regulate the activity and dimerization of FN3K. Human FN3K, which contains an equivalent P-loop Cys, was also redox sensitive, whereas ancestral bacterial FN3K homologs, which lack a P-loop Cys, were not. Furthermore, CRISPR-mediated knockout of FN3K in human liver cancer cells altered the abundance of redox metabolites, including an increase in glutathione. We propose that redox regulation evolved in FN3K homologs in response to changing cellular redox conditions. Our findings provide insights into the origin and evolution of redox regulation in the protein kinase superfamily and may open new avenues for targeting human FN3K in diabetic complications.


  • Organizational Affiliation
    • Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.

Macromolecule Content 

  • Total Structure Weight: 73.67 kDa 
  • Atom Count: 4,824 
  • Modeled Residue Count: 578 
  • Deposited Residue Count: 634 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein-ribulosamine 3-kinase, chloroplastic
A, B
317Arabidopsis thalianaMutation(s): 0 
Gene Names: At3g61080T27I15_170
EC: 2.7.1.172
UniProt
Find proteins for Q9LEW8 (Arabidopsis thaliana)
Explore Q9LEW8 
Go to UniProtKB:  Q9LEW8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LEW8
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP

Query on ADP



Download:Ideal Coordinates CCD File
C [auth A],
S [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
DMS

Query on DMS



Download:Ideal Coordinates CCD File
AA [auth B],
R [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
M [auth A],
Y [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free:  0.204 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.86α = 90
b = 163.64β = 90
c = 70.72γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-20
    Type: Initial release
  • Version 1.1: 2020-09-23
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-30
    Changes: Structure summary