› 5n4d

X-ray diffraction
1.62Å resolution

Prolyl oligopeptidase B from Galerina marginata bound to 25mer macrocyclization substrate - D661A mutant

Released:
DOI: 10.2210/pdb5n4d/pdb
PDB entry 5n4d coloured by chain, front view.
PDB entry 5n4d coloured by chain, side view.
PDB entry 5n4d coloured by chain, top view.
Source organism: Galerina marginata
Primary publication:
Characterization of a dual function macrocyclase enables design and use of efficient macrocyclization substrates.
Czekster CM, Ludewig H, McMahon SA, Naismith JH
Nat Commun 8 1045 (2017)
PMID: 29051530

Function and Biology Details

Reaction catalysed: 
Hydrolysis of --Pro-|- and to a lesser extent --Ala-|- in oligopeptides.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-100362 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Dual function macrocyclase-peptidase POPB Chains: A, B
Molecule details ›
Chains: A, B
Length: 730 amino acids
Theoretical weight: 81.83 KDa
Source organism: Galerina marginata
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: H2E7Q8 (Residues: 1-730; Coverage: 100%)
Gene names: GALMADRAFT_78538, POPB
Sequence domains:
Structure domains: alpha/beta hydrolase
Alpha-amanitin Chains: C, D
Molecule details ›
Chains: C, D
Length: 25 amino acids
Theoretical weight: 2.7 KDa
Source organism: Galerina marginata
Expression system: Not provided
UniProt:
  • Canonical: A0A067SLB9 (Residues: 11-35; Coverage: 71%)
Gene names: AMA1-1, GALMADRAFT_1387421

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P212121
Unit cell:
a: 99.04Å b: 114.88Å c: 141.31Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.198 0.234
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

5 review citations

Biosynthetic Proteases That Catalyze the Macrocyclization of Ribosomally Synthesized Linear Peptides.
Ongpipattanakul et al. (2018)
4 more

2 mentions without citation

Characterization of a dual function macrocyclase enables design and use of efficient macrocyclization substrates.
Czekster et al. (2017)
1 more