› 5xnc

X-ray diffraction
1.84Å resolution

Crystal structure of the branched-chain polyamine synthase (BpsA) in complex with N4-aminopropylspermidine and 5-methylthioadenosine

Released:
DOI: 10.2210/pdb5xnc/pdb
PDB entry 5xnc coloured by chain, front view.
PDB entry 5xnc coloured by chain, side view.
PDB entry 5xnc coloured by chain, top view.
Source organism: Thermococcus kodakarensis KOD1
Primary publication:
Active site geometry of a novel aminopropyltransferase for biosynthesis of hyperthermophile-specific branched-chain polyamine.
Hidese R, Tse KM, Kimura S, Mizohata E, Fujita J, Horai Y, Umezawa N, Higuchi T, Niitsu M, Oshima T, Imanaka T, Inoue T, Fujiwara S
FEBS J 284 3684-3701 (2017)
PMID: 28881427

Function and Biology Details

Reaction catalysed: 
(1a) S-adenosyl 3-(methylsulfanyl)propylamine + spermidine = S-methyl-5'-thioadenosine + N(4)-aminopropylspermidine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-177323 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
N(4)-bis(aminopropyl)spermidine synthase Chains: A, B, C, D, E, F, G
Molecule details ›
Chains: A, B, C, D, E, F, G
Length: 371 amino acids
Theoretical weight: 42.45 KDa
Source organism: Thermococcus kodakarensis KOD1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5JIZ3 (Residues: 1-351; Coverage: 100%)
Gene names: TK1691, bpsA
Sequence domains: Branched-chain polyamine synthase A C-terminal domain
Structure domains:

Ligands and Environments

6 bound ligands:
Ligand MTA 7 x MTA
Ligand N4P 7 x N4P
Ligand GOL 5 x GOL
Ligand FE 4 x FE
Ligand PEG 2 x PEG
Ligand EDO 3 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: C2
Unit cell:
a: 137.533Å b: 50.978Å c: 402.428Å
α: 90° β: 93.69° γ: 90°
R-values:
R R work R free
0.164 0.161 0.207
Expression system: Escherichia coli

Quick links

Citations

1 review citation

An overview of 25 years of research on Thermococcus kodakarensis, a genetically versatile model organism for archaeal research.
Rashid et al. (2020)
3 other articles

1 mention without citation

Active site geometry of a novel aminopropyltransferase for biosynthesis of hyperthermophile-specific branched-chain polyamine.
Hidese et al. (2017)