› 5cee

X-ray diffraction
2.5Å resolution

Malic enzyme from Candidatus Phytoplasma AYWB in complex with NAD and Mg2+

Released:
DOI: 10.2210/pdb5cee/pdb
PDB entry 5cee coloured by chain, front view.
PDB entry 5cee coloured by chain, side view.
PDB entry 5cee coloured by chain, top view.
Source organism: Aster yellows witches'-broom phytoplasma AYWB
Primary publication:
The crystal structure of the malic enzyme from Candidatus Phytoplasma reveals the minimal structural determinants for a malic enzyme.
Alvarez CE, Trajtenberg F, Larrieux N, Saigo M, Golic A, Andreo CS, Hogenhout SA, Mussi MA, Drincovich MF, Buschiazzo A
Acta Crystallogr D Struct Biol 74 332-340 (2018)
PMID: 29652260

Function and Biology Details

Reaction catalysed: 
(S)-malate + NAD(+) = pyruvate + CO(2) + NADH
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-173853 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
NAD-dependent malic enzyme Chain: A
Molecule details ›
Chain: A
Length: 413 amino acids
Theoretical weight: 44.32 KDa
Source organism: Aster yellows witches'-broom phytoplasma AYWB
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q2NK75 (Residues: 1-390; Coverage: 100%)
Gene names: AYWB_051, sfcA
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand NAD 1 x NAD
1 bound ligand:
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P3121
Unit cell:
a: 48.236Å b: 48.236Å c: 291.068Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.157 0.146 0.195
Expression system: Escherichia coli BL21(DE3)

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Citations

3 mentions without citation

A rotary mechanism for allostery in bacterial hybrid malic enzymes.
Harding et al. (2021)
2 more