5NUF | pdb_00005nuf

Cytosolic Malate Dehydrogenase 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.314 (Depositor), 0.188 (DCC) 
  • R-Value Work: 
    0.190 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5NUF

Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1093/jxb/erx396
  • Primary Citation Related Structures: 
    5NUE, 5NUF

  • 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. 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
    • Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.

Macromolecule Content 

  • Total Structure Weight: 111.26 kDa 
  • Atom Count: 8,406 
  • Modeled Residue Count: 991 
  • Deposited Residue Count: 996 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Malate dehydrogenase 1, cytoplasmic
A, B, C
332Arabidopsis thalianaMutation(s): 0 
Gene Names: MDH1At1g04410F19P19.13
EC: 1.1.1.37
UniProt
Find proteins for P93819 (Arabidopsis thaliana)
Explore P93819 
Go to UniProtKB:  P93819
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP93819
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD

Query on NAD



Download:Ideal Coordinates CCD File
AA [auth C],
D [auth A],
R [auth B]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
K [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
BA [auth C]
CA [auth C]
DA [auth C]
E [auth A]
F [auth A]
BA [auth C],
CA [auth C],
DA [auth C],
E [auth A],
F [auth A],
G [auth A],
S [auth B],
T [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
FA [auth C]
GA [auth C]
H [auth A]
HA [auth C]
I [auth A]
FA [auth C],
GA [auth C],
H [auth A],
HA [auth C],
I [auth A],
IA [auth C],
JA [auth C],
V [auth B],
W [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



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

Query on ACT



Download:Ideal Coordinates CCD File
EA [auth C],
U [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT

Query on FMT



Download:Ideal Coordinates CCD File
X [auth B]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
PEO

Query on PEO



Download:Ideal Coordinates CCD File
J [auth A],
KA [auth C]
HYDROGEN PEROXIDE
H2 O2
MHAJPDPJQMAIIY-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
L [auth A],
M [auth A],
Y [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.314 (Depositor), 0.188 (DCC) 
  • R-Value Work:  0.190 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.592α = 90
b = 118.545β = 90
c = 148.219γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-10
    Type: Initial release
  • Version 1.1: 2018-07-04
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description