› 8x35

X-ray diffraction
1.92Å resolution

Neryl diphosphate synthase from Solanum lycopersicum complexed with DMSAPP, IPP, and magnesium ion (form A)

Released:
DOI: 10.2210/pdb8x35/pdb
PDB entry 8x35 coloured by chain, front view.
PDB entry 8x35 coloured by chain, side view.
PDB entry 8x35 coloured by chain, top view.
Source organism: Solanum lycopersicum
Primary publication:
Structural-Functional Correlations between Unique N-terminal Region and C-terminal Conserved Motif in Short-chain cis-Prenyltransferase from Tomato.
Imaizumi R, Matsuura H, Yanai T, Takeshita K, Misawa S, Yamaguchi H, Sakai N, Miyagi-Inoue Y, Suenaga-Hiromori M, Waki T, Kataoka K, Nakayama T, Yamamoto M, Takahashi S, Yamashita S
Chembiochem e202300796 (2024)
PMID: 38225831

Function and Biology Details

Reaction catalysed: 
Prenyl diphosphate + isopentenyl diphosphate = diphosphate + neryl diphosphate
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-239590 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Dimethylallylcistransferase CPT1, chloroplastic Chains: A, B
Molecule details ›
Chains: A, B
Length: 305 amino acids
Theoretical weight: 34.8 KDa
Source organism: Solanum lycopersicum
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: C1K5M2 (Residues: 1-303; Coverage: 100%)
Gene names: CPT1, NDPS1
Sequence domains: Putative undecaprenyl diphosphate synthase

Ligands and Environments

6 bound ligands:
Ligand MG 2 x MG
Ligand IPE 1 x IPE
Ligand DST 1 x DST
Ligand PEG 1 x PEG
Ligand EDO 1 x EDO
Ligand DPO 2 x DPO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL32XU
Spacegroup: C2
Unit cell:
a: 98.31Å b: 49.23Å c: 121.39Å
α: 90° β: 91.067° γ: 90°
R-values:
R R work R free
0.221 0.219 0.257
Expression system: Escherichia coli BL21(DE3)

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