› 7x8k

X-ray diffraction
3Å resolution

Arabidopsis GDP-D-mannose pyrophosphorylase (VTC1) structure (product-bound)

Released:
DOI: 10.2210/pdb7x8k/pdb
PDB entry 7x8k coloured by chain, front view.
PDB entry 7x8k coloured by chain, side view.
PDB entry 7x8k coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Crystal Structures of Arabidopsis thaliana GDP-D-Mannose Pyrophosphorylase VITAMIN C DEFECTIVE 1.
Zhang C, Zhao S, Li YS, He C, Wang X, Liu L
OpenAccess logo Front Plant Sci 13 899738 (2022)
PMID: 35677252

Function and Biology Details

Reaction catalysed: 
GTP + alpha-D-mannose 1-phosphate = diphosphate + GDP-mannose
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127629 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Mannose-1-phosphate guanylyltransferase 1 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 376 amino acids
Theoretical weight: 41.34 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: O22287 (Residues: 1-361; Coverage: 100%)
Gene names: At2g39770, CYT1, EMB101, GMP1, HSN1, SOZ1, T5I7.7, VTC1
Sequence domains:

Ligands and Environments

4 bound ligands:
Ligand GDD 1 x GDD
Ligand FLC 2 x FLC
Ligand SO4 19 x SO4
Ligand PPV 2 x PPV
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: R32
Unit cell:
a: 185.113Å b: 185.113Å c: 371.752Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.235 0.234 0.26
Expression system: Escherichia coli

Quick links

Citations

1 mention without citation

Genetic and biochemical strategies for regulation of L-ascorbic acid biosynthesis in plants through the L-galactose pathway.
Castro et al. (2023)