5O3U

Structural characterization of the fast and promiscuous macrocyclase from plant - PCY1-S562A bound to Presegetalin F1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.3 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 13: 801-811

  • DOI: 10.1021/acschembio.8b00050
  • Primary Citation of Related Structures:  
    5O3U, 5O3V, 5O3W, 5O3X

  • 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 peptide leads ...

    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 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 nonamino acids, highlighting PCY1's potential in biocatalysis.


    Organizational Affiliation

    Division of Structural Biology , University of Oxford , Roosevelt Drive , Headington, Oxford OX3 7BN , United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peptide cyclase 1A, B, C, D724Gypsophila vaccariaMutation(s): 1 
Gene Names: Pcy1
EC: 3.4.21
UniProt
Find proteins for R4P353 (Gypsophila vaccaria)
Explore R4P353 
Go to UniProtKB:  R4P353
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupR4P353
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Putative presegetalin F1E [auth L],
F [auth M],
G [auth N],
H [auth O]
38Gypsophila vaccariaMutation(s): 0 
UniProt
Find proteins for F6LNM3 (Gypsophila vaccaria)
Explore F6LNM3 
Go to UniProtKB:  F6LNM3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF6LNM3
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.86α = 87.64
b = 85.82β = 78.32
c = 137.87γ = 89.52
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-07
    Type: Initial release
  • Version 1.1: 2018-03-28
    Changes: Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection
  • Version 1.3: 2019-11-27
    Changes: Derived calculations