5N4B | pdb_00005n4b

Prolyl oligopeptidase B from Galerina marginata bound to 25mer macrocyclization substrate - S577A mutant

• PDB DOI: https://doi.org/10.2210/pdb5N4B/pdb

• Classification: HYDROLASE
• Organism(s): Galerina marginata
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-02-10 Released: 2017-11-01 
• Deposition Author(s): Czekster, C.M., McMahon, S.A., Ludewig, H., Naismith, J.H.
• Funding Organization(s): European Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free: 
  0.181 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.155 (Depositor) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Characterization of a dual function macrocyclase enables design and use of efficient macrocyclization substrates.

Czekster, C.M., Ludewig, H., McMahon, S.A., Naismith, J.H.

(2017) Nat Commun 8: 1045-1045

• PubMed: 29051530 
• DOI: https://doi.org/10.1038/s41467-017-00862-4
• Primary Citation Related Structures: 
  5N4B, 5N4C, 5N4D, 5N4E, 5N4F


• 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.

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Organizational Affiliation: 
• Biomedical Sciences Research Complex, The University of St Andrews, North Haugh, St Andrews, K16 9ST, UK.
Biomedical Sciences Research Complex, The University of St Andrews, North Haugh, St Andrews, K16 9ST, UK. [e-mail].
Biotherapy Centre, Sichuan University, Chengdu, China. [e-mail].
RCaH, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, OX11 0FA, UK. [e-mail].
Division of Structural Biology, University of Oxford, Henry Wellcome Building for Genomic Medicine, Old Road Campus, Roosevelt Drive, Headington, Oxford, OX3 7BN, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 169.24 kDa 
• Atom Count: 13,794 
• Modeled Residue Count: 1,478 
• Deposited Residue Count: 1,512 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prolyl oligopeptidase	A, B	731	Galerina marginata	Mutation(s): 1  Gene Names: POPB EC: 3.4.21.26
UniProt
Find proteins for H2E7Q8 (Galerina marginata (strain CBS 339.88)) Explore H2E7Q8  Go to UniProtKB:  H2E7Q8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-amanitin proprotein	C [auth D], D [auth C]	25	Galerina marginata	Mutation(s): 0
UniProt
Find proteins for A0A067SLB9 (Galerina marginata (strain CBS 339.88)) Explore A0A067SLB9  Go to UniProtKB:  A0A067SLB9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free:  0.181 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.155 (Depositor) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.084	α = 90
b = 114.716	β = 90
c = 141.265	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-11-01 
Deposition Author(s): Czekster, C.M., McMahon, S.A., Ludewig, H., Naismith, J.H.

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Funding Organization	Location	Grant Number
European Research Council	United Kingdom	339367 NCB-TNT

Revision History  

• Version 1.0: 2017-11-01
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Database references
• Version 1.2: 2019-10-16
  Changes: Data collection
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Refinement description