5NUF

Cytosolic Malate Dehydrogenase 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Self-protection of cytosolic malate dehydrogenase against oxidative stress in Arabidopsis.

Huang, J.Niazi, A.K.Young, D.Rosado, L.A.Vertommen, D.Bodra, N.Abdelgawwad, M.R.Vignols, F.Wei, B.Wahni, K.Bashandy, T.Bariat, L.Van Breusegem, F.Messens, J.Reichheld, J.P.

(2018) J. Exp. Bot. 69: 3491-3505

  • DOI: 10.1093/jxb/erx396
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Plant malate dehydrogenase (MDH) isoforms are found in different cell compartments and function in key metabolic pathways. It is well known that the chloroplastic NADP-dependent MDH activities are strictly redox regulated and controlled by light. How ...

    Plant malate dehydrogenase (MDH) isoforms are found in different cell compartments and function in key metabolic pathways. It is well known that the chloroplastic NADP-dependent MDH activities are strictly redox regulated and controlled by light. However, redox dependence of other NAD-dependent MDH isoforms have been less studied. Here, we show by in vitro biochemical characterization that the major cytosolic MDH isoform (cytMDH1) is sensitive to H2O2 through sulfur oxidation of cysteines and methionines. CytMDH1 oxidation affects the kinetics, secondary structure, and thermodynamic stability of cytMDH1. Moreover, MS analyses and comparison of crystal structures between the reduced and H2O2-treated cytMDH1 further show that thioredoxin-reversible homodimerization of cytMDH1 through Cys330 disulfide formation protects the protein from overoxidation. Consistently, we found that cytosolic thioredoxins interact specifically with cytMDH in a yeast two-hybrid system. Importantly, we also show that cytosolic and chloroplastic, but not mitochondrial NAD-MDH activities are sensitive to H2O2 stress in Arabidopsis. NAD-MDH activities decreased both in a catalase2 mutant and in an NADP-thioredoxin reductase mutant, emphasizing the importance of the thioredoxin-reducing system to protect MDH from oxidation in vivo. We propose that the redox switch of the MDH activity contributes to adapt the cell metabolism to environmental constraints.


    Organizational Affiliation

    Center for Plant Systems Biology, VIB, Ghent, Belgium.,VIB-VUB Center for Structural Biology, Brussels, Belgium.,Laboratoire Génome et Développement des Plantes, Université de Perpignan Via Domitia, Perpignan, France.,de Duve Institute, Université Catholique de Louvain, Brussels, Belgium.,Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, Perpignan, France.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Brussels Center for Redox Biology, Brussels, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Malate dehydrogenase 1, cytoplasmic
A, B, C
332Arabidopsis thalianaMutation(s): 0 
Gene Names: MDH1
EC: 1.1.1.37
Find proteins for P93819 (Arabidopsis thaliana)
Go to Gene View: MDH1
Go to UniProtKB:  P93819
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FMT
Query on FMT

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B
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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B, C
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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A, B, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NAD
Query on NAD

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A, B, C
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
PEO
Query on PEO

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A, C
HYDROGEN PEROXIDE
H2 O2
MHAJPDPJQMAIIY-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.190 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 64.592α = 90.00
b = 118.545β = 90.00
c = 148.219γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-01-10
    Type: Initial release
  • Version 1.1: 2018-07-04
    Type: Data collection, Database references