5NUE

Cytosolic Malate Dehydrogenase 1 (peroxide-treated)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.148 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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: https://doi.org/10.1093/jxb/erx396
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Malate dehydrogenase 1, cytoplasmic332Arabidopsis 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Malate dehydrogenase 1, cytoplasmic332Arabidopsis 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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Malate dehydrogenase 1, cytoplasmic332Arabidopsis 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
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
D [auth A],
GA [auth C],
O [auth B]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
M [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
HA [auth C]
IA [auth C]
JA [auth C]
E [auth A],
F [auth A],
HA [auth C],
IA [auth C],
JA [auth C],
P [auth B],
Q [auth B],
R [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
KA [auth C]
S [auth B]
T [auth B]
G [auth A],
H [auth A],
KA [auth C],
S [auth B],
T [auth B],
U [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ETX
Query on ETX

Download Ideal Coordinates CCD File 
N [auth A]2-ETHOXYETHANOL
C4 H10 O2
ZNQVEEAIQZEUHB-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
EA [auth B],
FA [auth B],
RA [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
AA [auth B],
BA [auth B],
Z [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT
Query on FMT

Download Ideal Coordinates CCD File 
CA [auth B],
DA [auth B],
L [auth A],
PA [auth C],
QA [auth C]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
PEO
Query on PEO

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth A]
LA [auth C]
MA [auth C]
I [auth A],
J [auth A],
K [auth A],
LA [auth C],
MA [auth C],
NA [auth C],
OA [auth C],
V [auth B],
W [auth B],
X [auth B],
Y [auth B]
HYDROGEN PEROXIDE
H2 O2
MHAJPDPJQMAIIY-UHFFFAOYSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
CSD
Query on CSD
B
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
SME
Query on SME
B
L-PEPTIDE LINKINGC5 H11 N O3 SMET
CSO
Query on CSO
C
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.148 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.598α = 90
b = 118.374β = 90
c = 148.489γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Centre National de la Recherche Scientifique and the Agence Nationale de la RechercheFranceANR-Blanc Cynthiol 12-BSV6-0011
VIBBelgium--
Vrije Universiteit BrusselBelgiumSPR34
Research Foundation Flanders (FWO)Belgium--

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-07-04
    Changes: Data collection, Database references