› 6dby

X-ray diffraction
2Å resolution

Crystal structure of Nudix 1 from Arabidopsis thaliana

Released:
DOI: 10.2210/pdb6dby/pdb
PDB entry 6dby coloured by chain, front view.
PDB entry 6dby coloured by chain, side view.
PDB entry 6dby coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Contribution of isopentenyl phosphate to plant terpenoid metabolism.
Henry LK, Thomas ST, Widhalm JR, Lynch JH, Davis TC, Kessler SA, Bohlmann J, Noel JP, Dudareva N
Nat Plants 4 721-729 (2018)
PMID: 30127411

Function and Biology Details

Reactions catalysed: 
NAD(H) + H(2)O = AMP + NMN(H)
8-oxo-dGTP + H(2)O = 8-oxo-dGMP + diphosphate
7,8-dihydroneopterin 3'-triphosphate + H(2)O = 7,8-dihydroneopterin 3'-phosphate + diphosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-189940 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nudix hydrolase 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 150 amino acids
Theoretical weight: 16.66 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9CA40 (Residues: 1-147; Coverage: 100%)
Gene names: At1g68760, F14K14.13, NUDT1, NUDX1
Sequence domains: NUDIX domain
Structure domains: Nucleoside Triphosphate Pyrophosphohydrolase

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.1
Spacegroup: P212121
Unit cell:
a: 36.19Å b: 73.07Å c: 116.54Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.188 0.186 0.221
Expression system: Escherichia coli

Quick links

Citations

11 review citations

Terpene Synthases as Metabolic Gatekeepers in the Evolution of Plant Terpenoid Chemical Diversity.
Karunanithi et al. (2019)
10 more