› 6hsp

X-ray diffraction
1.73Å resolution

Crystal structure of the zebrafish peroxisomal SCP2-thiolase (type-1) in complex with CoA and octanoyl-CoA

Released:
DOI: 10.2210/pdb6hsp/pdb
Model geometry
Fit model/data
PDB entry 6hsp coloured by chain, front view.
PDB entry 6hsp coloured by chain, side view.
PDB entry 6hsp coloured by chain, top view.
Source organism: Danio rerio
Primary publication:
The peroxisomal zebrafish SCP2-thiolase (type-1) is a weak transient dimer as revealed by crystal structures and native mass spectrometry.
Kiema TR, Thapa CJ, Laitaoja M, Schmitz W, Maksimainen MM, Fukao T, Rouvinen J, Jänis J, Wierenga RK
Biochem J 476 307-332 (2019)
PMID: 30573650

Function and Biology Details

Reactions catalysed: 
Myristoyl-CoA + acetyl-CoA = 3-oxopalmitoyl-CoA + CoA
(1a) [acetyl-CoA C-acyltransferase]-S-acyl-L-cyteine + acetyl-CoA = 3-oxoacyl-CoA + [acetyl-CoA C-acyltransferase]-L-cyteine
3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholanoyl-CoA + propanoyl-CoA = CoA + 3-alpha,7-alpha,12-alpha-trihydroxy-24-oxo-5-beta-cholestanoyl-CoA
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-180120 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Sterol carrier protein 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 414 amino acids
Theoretical weight: 45.11 KDa
Source organism: Danio rerio
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q6P4V5 (Residues: 1-406; Coverage: 76%)
Gene names: scp2, scp2a, zgc:77634
Sequence domains:

Ligands and Environments


Cofactor: Ligand COA 1 x COA

Cofactor: Ligand CO8 1 x CO8
1 bound ligand:
Ligand GOL 4 x GOL
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: C2
Unit cell:
a: 132.18Å b: 81.32Å c: 96.63Å
α: 90° β: 126.08° γ: 90°
R-values:
R R work R free
0.192 0.19 0.227
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Mutation update on ACAT1 variants associated with mitochondrial acetoacetyl-CoA thiolase (T2) deficiency.
Abdelkreem et al. (2019)
5 other articles