› 5gp0

X-ray diffraction
1.7Å resolution

Crystal structure of geraniol-NUDX1 complex

Released:
DOI: 10.2210/pdb5gp0/pdb
PDB entry 5gp0 coloured by chain, front view.
PDB entry 5gp0 coloured by chain, side view.
PDB entry 5gp0 coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Structural Insights into the Substrate Recognition Mechanism of Arabidopsis GPP-Bound NUDX1 for Noncanonical Monoterpene Biosynthesis.
Liu J, Guan Z, Liu H, Qi L, Zhang D, Zou T, Yin P
Mol Plant 11 218-221 (2018)
PMID: 29066356

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

Assemblies composition:
homo tetramer
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-189940 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nudix hydrolase 1 Chains: A, E, F, I
Molecule details ›
Chains: A, E, F, I
Length: 149 amino acids
Theoretical weight: 16.58 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21(DE3)
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

2 bound ligands:
Ligand GOL 2 x GOL
Ligand GPP 4 x GPP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Unit cell:
a: 69.761Å b: 83.582Å c: 116.36Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.184 0.183 0.21
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 citation in other articles

Contribution of isopentenyl phosphate to plant terpenoid metabolism.
Henry et al. (2018)
4 more