› 4twm

X-ray diffraction
2.11Å resolution

Crystal structure of dioscorin from Dioscorea japonica

Released:
DOI: 10.2210/pdb4twm/pdb
PDB entry 4twm coloured by chain, front view.
PDB entry 4twm coloured by chain, side view.
PDB entry 4twm coloured by chain, top view.
Source organism: Dioscorea japonica
Primary publication:
Yam Tuber Storage Protein Reduces Plant Oxidants Using the Coupled Reactions as Carbonic Anhydrase and Dehydroascorbate Reductase.
Xue YL, Miyakawa T, Nakamura A, Hatano K, Sawano Y, Tanokura M
Mol Plant 8 1115-8 (2015)
PMID: 25747844

Function and Biology Details

Reactions catalysed: 
NADH + 2 monodehydroascorbate = NAD(+) + 2 ascorbate
H(2)CO(3) = CO(2) + H(2)O
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-501194 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Dioscorin dioA3 Chains: A, B
Molecule details ›
Chains: A, B
Length: 246 amino acids
Theoretical weight: 28.22 KDa
Source organism: Dioscorea japonica
Expression system: Escherichia coli
UniProt:
  • Canonical: A7MAQ2 (Residues: 26-271; Coverage: 98%)
Gene names: dio5, dioA3
Sequence domains: Eukaryotic-type carbonic anhydrase
Structure domains: Alpha carbonic anhydrase

Ligands and Environments

1 bound ligand:
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: C2221
Unit cell:
a: 83.47Å b: 156.77Å c: 83.56Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.212 0.209 0.272
Expression system: Escherichia coli

Quick links

Citations

6 citation in other articles

Chemical components and emulsification properties of mucilage from Dioscorea opposita Thunb.
Ma et al. (2017)
5 more

2 mentions without citation

Functional properties of Chinese yam (Dioscorea opposita Thunb. cv. Baiyu) soluble protein.
Hu et al. (2018)
1 more