8JE4

Crystal structure of LimF prenyltransferase (H239G/W273T mutant) bound with the thiodiphosphate moiety of farnesyl S-thiolodiphosphate (FSPP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.211 

Starting Model: experimental
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Literature

Switching Prenyl Donor Specificities of Cyanobactin Prenyltransferases.

Zhang, Y.Hamada, K.Satake, M.Sengoku, T.Goto, Y.Suga, H.

(2023) J Am Chem Soc 145: 23893-23898

  • DOI: https://doi.org/10.1021/jacs.3c07373
  • Primary Citation of Related Structures:  
    8JE4

  • PubMed Abstract: 

    Prenyltransferases in cyanobactin biosynthesis are of growing interest as peptide alkylation biocatalysts, but their prenylation modes characterized so far have been limited to dimethylallylation (C5) or geranylation (C10). Here we engaged in structure-guided engineering of the prenyl-binding pocket of a His- C2 -geranyltransferase LimF to modulate its prenylation mode. Contraction of the pocket by a single mutation led to a His- C2 -dimethylallyltransferase. More importantly, pocket expansion by a double mutation successfully repurposed LimF for farnesylation (C15), which is an unprecedented mode in this family. Furthermore, the obtained knowledge of the essential residues to construct the farnesyl-binding pocket has allowed for rational design of a Tyr- O -farnesyltransferase by a triple mutation of a Tyr- O -dimethylallyltransferase PagF. These results provide an approach to manipulate the prenyl specificity of cyanobactin prenyltransferases, broadening the chemical space covered by this class of enzymes and expanding the toolbox of peptide alkylation biocatalysts.


  • Organizational Affiliation

    Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
prenyltransferase, LimF
A, B
302Limnothrix sp. CACIAM 69dMutation(s): 2 
Gene Names: BJG00_018450
UniProt
Find proteins for A0A372DCN7 (Limnothrix sp. CACIAM 69d)
Explore A0A372DCN7 
Go to UniProtKB:  A0A372DCN7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A372DCN7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.98α = 90
b = 47.88β = 117.656
c = 89.46γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-08
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Database references