5O3X

Structural characterization of the fast and promiscuous macrocyclase from plant - apo PCY1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Characterization of the fast and promiscuous macrocyclase from plant PCY1 enables the use of simple substrates.

Ludewig, H.Czekster, C.M.Oueis, E.Munday, E.S.Arshad, M.Synowsky, S.A.Bent, A.F.Naismith, J.H.

(2018) ACS Chem. Biol. --: --

  • DOI: 10.1021/acschembio.8b00050
  • Primary Citation of Related Structures:  5O3U, 5O3V, 5O3W

  • PubMed Abstract: 
  • Cyclic ribosomally derived peptides possess diverse bioactivities and are currently of major interest in drug development. However, it can be chemically challenging to synthesize these molecules, hindering the diversification and testing of cyclic pe ...

    Cyclic ribosomally derived peptides possess diverse bioactivities and are currently of major interest in drug development. However, it can be chemically challenging to synthesize these molecules, hindering the diversification and testing of cyclic peptide leads. Enzymes used in vitro offer a solution to this, however peptide macrocyclization remains the bottleneck. PCY1, involved in the biosynthesis of plant orbitides, belongs to the class of prolyl oligopeptidases and natively displays substrate promiscuity. PCY1 is a promising candidate for in vitro utilization but its substrates require an 11 to 16 residue C-terminal recognition tail. We have characterized PCY1 both kinetically and structurally with multiple substrate complexes revealing for the molecular basis of recognition and catalysis. Using these insights, we have identified a three residue C-terminal extension that replaces the natural recognition tail permitting PCY1 to operate on synthetic substrates. We demonstrate that PCY1 can macrocyclize a variety of substrates with this short tail, including unnatural amino acids and non-amino acids, highlighting PCY1's potential in biocatalysis.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptide cyclase 1
A, B
724Vaccaria hispanicaGene Names: Pcy1
Find proteins for R4P353 (Vaccaria hispanica)
Go to UniProtKB:  R4P353
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CAC
Query on CAC

Download SDF File 
Download CCD File 
A, B
CACODYLATE ION
dimethylarsinate
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.216 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 275.580α = 90.00
b = 60.850β = 92.65
c = 88.040γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
xia2data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
European UnionUnited Kingdom339367 NCB-TNT
Biotechnology and Biological Sciences Research CouncilUnited Kingdom--

Revision History 

  • Version 1.0: 2018-02-07
    Type: Initial release