5TU5

PagF prenyltransferase with Tyr-Tyr-Tyr and DMSPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Molecular basis for the broad substrate selectivity of a peptide prenyltransferase.

Hao, Y.Pierce, E.Roe, D.Morita, M.McIntosh, J.A.Agarwal, V.Cheatham, T.E.Schmidt, E.W.Nair, S.K.

(2016) Proc Natl Acad Sci U S A 113: 14037-14042

  • DOI: https://doi.org/10.1073/pnas.1609869113
  • Primary Citation of Related Structures:  
    5TTY, 5TU4, 5TU5, 5TU6

  • PubMed Abstract: 

    The cyanobactin prenyltransferases catalyze a series of known or unprecedented reactions on millions of different substrates, with no easily observable recognition motif and exquisite regioselectivity. Here we define the basis of broad substrate tolerance for the otherwise uncharacterized TruF family. We determined the structures of the Tyr-prenylating enzyme PagF, in complex with an isoprenoid donor analog and a panel of linear and macrocyclic peptide substrates. Unexpectedly, the structures reveal a truncated barrel fold, wherein binding of large peptide substrates is necessary to complete a solvent-exposed hydrophobic pocket to form the catalytically competent active site. Kinetic, mutational, chemical, and computational analyses revealed the structural basis of selectivity, showing a small motif within peptide substrates that is sufficient for recognition by the enzyme. Attaching this 2-residue motif to two random peptides results in their isoprenylation by PagF, demonstrating utility as a general biocatalytic platform for modifications on any peptide substrate.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PagF prenyltransferase300Planktothrix agardhii NIES-596Mutation(s): 0 
Gene Names: pagF
UniProt
Find proteins for F5B6Z0 (Planktothrix agardhii NIES-596)
Explore F5B6Z0 
Go to UniProtKB:  F5B6Z0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF5B6Z0
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TYR-TYR-TYR3synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DST
Query on DST

Download Ideal Coordinates CCD File 
C [auth A]DIMETHYLALLYL S-THIOLODIPHOSPHATE
C5 H12 O6 P2 S
ZWFWSISPSBLNGO-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.042α = 90
b = 117.042β = 90
c = 43.8γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-30
    Type: Initial release
  • Version 1.1: 2016-12-07
    Changes: Derived calculations
  • Version 1.2: 2016-12-21
    Changes: Database references
  • Version 2.0: 2019-10-02
    Changes: Data collection, Non-polymer description, Structure summary
  • Version 2.1: 2024-03-06
    Changes: Data collection, Database references, Derived calculations, Structure summary