› 4bmk

X-ray diffraction
1.62Å resolution

Serine Palmitoyltransferase K265A from S. paucimobilis with bound PLP- Myriocin Aldimine

Released:
DOI: 10.2210/pdb4bmk/pdb
PDB entry 4bmk coloured by chain, front view.
PDB entry 4bmk coloured by chain, side view.
PDB entry 4bmk coloured by chain, top view.
Source organism: Sphingomonas paucimobilis
Primary publication:
The chemical basis of serine palmitoyltransferase inhibition by myriocin.
Wadsworth JM, Clarke DJ, McMahon SA, Lowther JP, Beattie AE, Langridge-Smith PR, Broughton HB, Dunn TM, Naismith JH, Campopiano DJ
J Am Chem Soc 135 14276-85 (2013)
PMID: 23957439

Function and Biology Details

Reaction catalysed: 
Palmitoyl-CoA + L-serine = CoA + 3-dehydro-D-sphinganine + CO(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188138 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Serine palmitoyltransferase Chains: A, B
Molecule details ›
Chains: A, B
Length: 442 amino acids
Theoretical weight: 47.34 KDa
Source organism: Sphingomonas paucimobilis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q93UV0 (Residues: 2-420; Coverage: 100%)
Gene names: HKX06_04505, I6G38_17245, SPT1, spt
Sequence domains: Aminotransferase class I and II
Structure domains:

Ligands and Environments


Cofactor: Ligand PLP 2 x PLP
2 bound ligands:
Ligand MYB 2 x MYB
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P212121
Unit cell:
a: 61.91Å b: 98.71Å c: 133.19Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.189 0.211
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

15 review citations

Sphingolipids and their metabolism in physiology and disease.
Hannun et al. (2018)
14 more

3 mentions without citation

Membrane disruption of Fusarium oxysporum f. sp. niveum induced by myriocin from Bacillus amyloliquefaciens LZN01.
Wang et al. (2021)
2 more