5UW7

PCY1 Y481F Variant in Complex with Follower Peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Characterization of the macrocyclase involved in the biosynthesis of RiPP cyclic peptides in plants.

Chekan, J.R.Estrada, P.Covello, P.S.Nair, S.K.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: 6551-6556

  • DOI: 10.1073/pnas.1620499114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Enzymes that can catalyze the macrocyclization of linear peptide substrates have long been sought for the production of libraries of structurally diverse scaffolds via combinatorial gene assembly as well as to afford rapid in vivo screening methods. ...

    Enzymes that can catalyze the macrocyclization of linear peptide substrates have long been sought for the production of libraries of structurally diverse scaffolds via combinatorial gene assembly as well as to afford rapid in vivo screening methods. Orbitides are plant ribosomally synthesized and posttranslationally modified peptides (RiPPs) of various sizes and topologies, several of which are shown to be biologically active. The diversity in size and sequence of orbitides suggests that the corresponding macrocyclases may be ideal catalysts for production of cyclic peptides. Here we present the biochemical characterization and crystal structures of the plant enzyme PCY1 involved in orbitide macrocyclization. These studies demonstrate how the PCY1 S9A protease fold has been adapted for transamidation, rather than hydrolysis, of acyl-enzyme intermediates to yield cyclic products. Notably, PCY1 uses an unusual strategy in which the cleaved C-terminal follower peptide from the substrate stabilizes the enzyme in a productive conformation to facilitate macrocyclization of the N-terminal fragment. The broad substrate tolerance of PCY1 can be exploited as a biotechnological tool to generate structurally diverse arrays of macrocycles, including those with nonproteinogenic elements.


    Organizational Affiliation

    Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptide cyclase 1
A, B
750Gypsophila vaccariaMutation(s): 0 
Gene Names: Pcy1
Find proteins for R4P353 (Gypsophila vaccaria)
Go to UniProtKB:  R4P353
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Presegetalin A1
C, D
19Gypsophila vaccariaMutation(s): 0 
Find proteins for F6LNL5 (Gypsophila vaccaria)
Go to UniProtKB:  F6LNL5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.236 
  • Space Group: P 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 86.947α = 90.00
b = 59.629β = 93.12
c = 134.164γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
AutoPROCdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2017-06-21
    Type: Database references
  • Version 1.2: 2017-07-05
    Type: Database references