› 8bit

X-ray diffraction
3.1Å resolution

Crystal structure of acyl-CoA synthetase from Metallosphaera sedula in complex with Coenzyme A and acetyl-AMP

Released:
DOI: 10.2210/pdb8bit/pdb
PDB entry 8bit coloured by chain, front view.
PDB entry 8bit coloured by chain, side view.
PDB entry 8bit coloured by chain, top view.
Source organism: Metallosphaera sedula DSM 5348
Primary publication:
Adapting an acyl CoA ligase from Metallosphaera sedula for lactam formation by structure-guided protein engineering
Capra N, Lelievre C, Toure O, Fossey-Jouenne A, Vergne-Vaxelaire C, Janssen DB, Thunnissen AMWH, Zaparucha A
Front Catal 4 (2024)

Function and Biology Details

Reactions catalysed: 
ATP + acetate + CoA = AMP + diphosphate + acetyl-CoA
ATP + propanoate + CoA = AMP + diphosphate + propanoyl-CoA
ATP + a medium-chain fatty acid + CoA = AMP + diphosphate + a medium-chain acyl-CoA
ATP + 4-hydroxybutanoate + CoA = AMP + diphosphate + 4-hydroxybutanoyl-CoA
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-239848 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
4-hydroxybutyrate--CoA ligase 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 570 amino acids
Theoretical weight: 65.22 KDa
Source organism: Metallosphaera sedula DSM 5348
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A4YDT1 (Residues: 2-564; Coverage: 100%)
Gene name: Msed_0406
Sequence domains:

Ligands and Environments


Cofactor: Ligand COA 2 x COA
1 bound ligand:
Ligand 6R9 2 x 6R9
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: C2
Unit cell:
a: 105.806Å b: 93.19Å c: 131.685Å
α: 90° β: 91.12° γ: 90°
R-values:
R R work R free
0.214 0.21 0.277
Expression system: Escherichia coli BL21(DE3)

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