› 5nue

X-ray diffraction
1.35Å resolution

Cytosolic Malate Dehydrogenase 1 (peroxide-treated)

Released:
DOI: 10.2210/pdb5nue/pdb
PDB entry 5nue coloured by chain, front view.
PDB entry 5nue coloured by chain, side view.
PDB entry 5nue coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Self-protection of cytosolic malate dehydrogenase against oxidative stress in Arabidopsis.
Huang J, Niazi AK, Young D, Rosado LA, Vertommen D, Bodra N, Abdelgawwad MR, Vignols F, Wei B, Wahni K, Bashandy T, Bariat L, Van Breusegem F, Messens J, Reichheld JP
J Exp Bot 69 3491-3505 (2018)
PMID: 29194485

Function and Biology Details

Reaction catalysed: 
(S)-malate + NAD(+) = oxaloacetate + NADH
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-161088 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Malate dehydrogenase 1, cytoplasmic Chain: A
Molecule details ›
Chain: A
Length: 332 amino acids
Theoretical weight: 35.61 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P93819 (Residues: 1-332; Coverage: 100%)
Gene names: At1g04410, F19P19.13, MDH1
Sequence domains:
Structure domains:
Malate dehydrogenase 1, cytoplasmic Chain: B
Molecule details ›
Chain: B
Length: 332 amino acids
Theoretical weight: 35.67 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P93819 (Residues: 1-332; Coverage: 100%)
Gene names: At1g04410, F19P19.13, MDH1
Sequence domains:
Structure domains:
Malate dehydrogenase 1, cytoplasmic Chain: C
Molecule details ›
Chain: C
Length: 332 amino acids
Theoretical weight: 35.64 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P93819 (Residues: 1-332; Coverage: 100%)
Gene names: At1g04410, F19P19.13, MDH1
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand NAD 3 x NAD
8 bound ligands:
Ligand SO4 8 x SO4
Ligand GOL 6 x GOL
Ligand PEO 11 x PEO
Ligand FMT 5 x FMT
Ligand TRS 1 x TRS
Ligand ETX 1 x ETX
Ligand ACT 3 x ACT
Ligand EDO 3 x EDO
3 modified residues:
Ligand SME 3 x SME
Ligand CSD 1 x CSD
Ligand CSO 1 x CSO

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 2
Unit cell:
a: 64.598Å b: 118.374Å c: 148.489Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.148 0.146 0.18
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

7 review citations

Contemporary proteomic strategies for cysteine redoxome profiling.
Willems et al. (2021)
6 more