› 4pkf

X-ray diffraction
2Å resolution

Benzylsuccinate synthase alpha-beta-gamma complex

Released:
DOI: 10.2210/pdb4pkf/pdb
PDB entry 4pkf coloured by chain, front view.
PDB entry 4pkf coloured by chain, side view.
PDB entry 4pkf coloured by chain, top view.
Source organism: Thauera aromatica
Primary publication:
Structures of benzylsuccinate synthase elucidate roles of accessory subunits in glycyl radical enzyme activation and activity.
Funk MA, Judd ET, Marsh EN, Elliott SJ, Drennan CL
Proc Natl Acad Sci U S A 111 10161-6 (2014)
PMID: 24982148

Function and Biology Details

Reaction catalysed: 
Toluene + fumarate = benzylsuccinate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-130613 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Benzylsuccinate synthase alpha subunit Chain: A
Molecule details ›
Chain: A
Length: 878 amino acids
Theoretical weight: 99.12 KDa
Source organism: Thauera aromatica
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O68395 (Residues: 1-864; Coverage: 100%)
Gene name: tutD
Sequence domains:
Benzylsuccinate synthase beta subunit domain-containing protein Chain: B
Molecule details ›
Chain: B
Length: 81 amino acids
Theoretical weight: 9.3 KDa
Source organism: Thauera aromatica
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O68396 (Residues: 1-81; Coverage: 100%)
Gene name: tutG
Sequence domains: Benzylsuccinate synthase beta subunit
Structure domains: High-Potential Iron-Sulfur Protein; Chain A
TutF Chain: C
Molecule details ›
Chain: C
Length: 60 amino acids
Theoretical weight: 6.87 KDa
Source organism: Thauera aromatica
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O68394 (Residues: 1-60; Coverage: 100%)
Gene name: tutF
Sequence domains: BssC/TutF protein

Ligands and Environments

3 bound ligands:
Ligand GOL 3 x GOL
Ligand CL 1 x CL
Ligand SF4 1 x SF4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.2
Spacegroup: I222
Unit cell:
a: 113.424Å b: 120.421Å c: 136.048Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.131 0.129 0.177
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

New tricks for the glycyl radical enzyme family.
Backman et al. (2017)
4 more

5 mentions without citation

The origin and evolution of ribonucleotide reduction.
Lundin et al. (2015)
4 more