› 5hp8

X-ray diffraction
2.3Å resolution

Crystal structures of RidA in complex with pyruvate

Released:
DOI: 10.2210/pdb5hp8/pdb
PDB entry 5hp8 coloured by chain, front view.
PDB entry 5hp8 coloured by chain, side view.
PDB entry 5hp8 coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Crystal structures of RidA, an important enzyme for the prevention of toxic side products.
Liu X, Zeng J, Chen X, Xie W
Sci Rep 6 30494 (2016)
PMID: 27458092

Function and Biology Details

Reaction catalysed: 
2-iminobutanoate + H(2)O = 2-oxobutanoate + NH(3)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188237 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Reactive Intermediate Deaminase A, chloroplastic Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 124 amino acids
Theoretical weight: 13.23 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q94JQ4 (Residues: 68-187; Coverage: 64%)
Gene names: At3g20390, MQC12.15, RIDA
Sequence domains: Endoribonuclease L-PSP
Structure domains: RutC-like

Ligands and Environments

1 bound ligand:
Ligand PYR 3 x PYR
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: Agilent SuperNova
Spacegroup: P1
Unit cell:
a: 40.325Å b: 46.251Å c: 46.375Å
α: 111.44° β: 107.74° γ: 106.26°
R-values:
R R work R free
0.206 0.204 0.238
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Nitric Oxide Modulates Metabolic Processes in the Tumor Immune Microenvironment.
McGinity et al. (2021)
6 other articles

2 mentions without citation

RidA Proteins Protect against Metabolic Damage by Reactive Intermediates.
Irons et al. (2020)
1 more