5N4F

Prolyl oligopeptidase B from Galerina marginata - apo protein

Summary for 5N4F

• Entry DOI: 10.2210/pdb5n4f/pdb
• Descriptor: Prolyl oligopeptidase, GLYCEROL (3 entities in total)
• Functional Keywords: amanitin biosynthesis, prolyl oligopeptidase, macrocyclase, peptidase, beta-propeller, open form, hydrolase
• Biological source: Galerina marginata
• Total number of polymer chains: 1
• Total formula weight: 82060.79

Authors

Czekster, C.M.,McMahon, S.A.,Ludewig, H.,Naismith, J.H. (deposition date: 2017-02-10, release date: 2017-11-01, Last modification date: 2024-05-08)

Primary citation

Czekster, C.M.,Ludewig, H.,McMahon, S.A.,Naismith, J.H.
Characterization of a dual function macrocyclase enables design and use of efficient macrocyclization substrates.
Nat Commun, 8:1045-1045, 2017

PubMed 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.

PubMed: 29051530
DOI: 10.1038/s41467-017-00862-4

Experimental method

X-RAY DIFFRACTION (2.4 Å)