› 8h29

X-ray diffraction
1.45Å resolution

Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with L-threonine

Released:
DOI: 10.2210/pdb8h29/pdb
PDB entry 8h29 coloured by chain, front view.
PDB entry 8h29 coloured by chain, side view.
PDB entry 8h29 coloured by chain, top view.
Source organism: Sphingobacterium multivorum
Primary publication:
Structural insights into the substrate recognition of serine palmitoyltransferase from Sphingobacterium multivorum.
Ikushiro H, Murakami T, Takahashi A, Katayama A, Sawai T, Goto H, Koolath S, Murai Y, Monde K, Miyahara I, Kamiya N, Yano T
J Biol Chem 299 104684 (2023)
PMID: 37030501

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-108244 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Serine palmitoyltransferase Chain: A
Molecule details ›
Chain: A
Length: 399 amino acids
Theoretical weight: 43.82 KDa
Source organism: Sphingobacterium multivorum
Expression system: Escherichia coli
UniProt:
  • Canonical: A7BFV6 (Residues: 1-399; Coverage: 100%)
Gene names: I6J33_20140, NCTC11343_02561, SPHINGO8BC_150128, spt
Sequence domains: Aminotransferase class I and II

Ligands and Environments

2 bound ligands:
Ligand 2BO 1 x 2BO
Ligand EDO 9 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P41212
Unit cell:
a: 61.083Å b: 61.083Å c: 207.89Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.148 0.145 0.174
Expression system: Escherichia coli

Quick links

Citations

1 mention without citation

Structural insights into the substrate recognition of serine palmitoyltransferase from Sphingobacterium multivorum.
Ikushiro et al. (2023)