spacer
spacer

PDBsum entry 5n4f

Go to PDB code: 
protein ligands links
Hydrolase PDB id
5n4f

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chain
703 a.a.
Ligands
GOL ×2
Waters ×187
PDB id:
5n4f
Name: Hydrolase
Title: Prolyl oligopeptidase b from galerina marginata - apo protein
Structure: Prolyl oligopeptidase. Chain: a. Engineered: yes
Source: Galerina marginata. Organism_taxid: 109633. Gene: popb. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Resolution:
2.40Å     R-factor:   0.218     R-free:   0.254
Authors: C.M.Czekster,S.A.Mcmahon,H.Ludewig,J.H.Naismith
Key ref: C.M.Czekster et al. (2017). Characterization of a dual function macrocyclase enables design and use of efficient macrocyclization substrates. Nat Commun, 8, 1045. PubMed id: 29051530
Date:
10-Feb-17     Release date:   01-Nov-17    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
H2E7Q8  (POPB_GALM3) -  Dual function macrocyclase-peptidase POPB from Galerina marginata (strain CBS 339.88)
Seq:
Struc:
 
Seq:
Struc:
730 a.a.
703 a.a.
Key:    PfamA domain  Secondary structure

 Enzyme reactions 
   Enzyme class: E.C.3.4.21.26  - prolyl oligopeptidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of Pro-|-Xaa >> Ala-|-Xaa in oligopeptides.

 

 
Nat Commun 8:1045 (2017)
PubMed id: 29051530  
 
 
Characterization of a dual function macrocyclase enables design and use of efficient macrocyclization substrates.
C.M.Czekster, H.Ludewig, S.A.McMahon, J.H.Naismith.
 
  ABSTRACT  
 
Peptide macrocycles are promising therapeutic molecules because they are protease resistant, structurally rigid, membrane permeable, and capable of modulating protein-protein interactions. Here, we report the characterization of the dual function macrocyclase-peptidase enzyme involved in the biosynthesis of the highly toxic amanitin toxin family of macrocycles. The enzyme first removes 10 residues from the N-terminus of a 35-residue substrate. Conformational trapping of the 25 amino-acid peptide forces the enzyme to release this intermediate rather than proceed to macrocyclization. The enzyme rebinds the 25 amino-acid peptide in a different conformation and catalyzes macrocyclization of the N-terminal eight residues. Structures of the enzyme bound to both substrates and biophysical analysis characterize the different binding modes rationalizing the mechanism. Using these insights simpler substrates with only five C-terminal residues were designed, allowing the enzyme to be more effectively exploited in biotechnology.
 

 

spacer

spacer