6VKZ

Crystal Structure of the N-prenyltransferase DabA in Complex with GSPP and Mg2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Algal neurotoxin biosynthesis repurposes the terpene cyclase structural fold into anN-prenyltransferase.

Chekan, J.R.McKinnie, S.M.K.Noel, J.P.Moore, B.S.

(2020) Proc Natl Acad Sci U S A 117: 12799-12805

  • DOI: https://doi.org/10.1073/pnas.2001325117
  • Primary Citation of Related Structures:  
    6VKZ, 6VL0, 6VL1

  • PubMed Abstract: 

    Prenylation is a common biological reaction in all domains of life wherein prenyl diphosphate donors transfer prenyl groups onto small molecules as well as large proteins. The enzymes that catalyze these reactions are structurally distinct from ubiquitous terpene cyclases that, instead, assemble terpenes via intramolecular rearrangements of a single substrate. Herein, we report the structure and molecular details of a new family of prenyltransferases from marine algae that repurposes the terpene cyclase structural fold for the N -prenylation of glutamic acid during the biosynthesis of the potent neurochemicals domoic acid and kainic acid. We solved the X-ray crystal structure of the prenyltransferase found in domoic acid biosynthesis, DabA, and show distinct active site binding modifications that remodel the canonical magnesium (Mg 2+ )-binding motif found in terpene cyclases. We then applied our structural knowledge of DabA and a homologous enzyme from the kainic acid biosynthetic pathway, KabA, to reengineer their isoprene donor specificities (geranyl diphosphate [GPP] versus dimethylallyl diphosphate [DMAPP]) with a single amino acid change. While diatom DabA and seaweed KabA enzymes share a common evolutionary lineage, they are distinct from all other terpene cyclases, suggesting a very distant ancestor to the larger terpene synthase family.


  • Organizational Affiliation

    Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DabA441Pseudo-nitzschia multiseriesMutation(s): 0 
Gene Names: dabA
EC: 2.5.1
UniProt
Find proteins for A0A386KZ50 (Pseudo-nitzschia multiseries)
Explore A0A386KZ50 
Go to UniProtKB:  A0A386KZ50
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A386KZ50
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.286α = 90
b = 124.286β = 90
c = 114.483γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
autoPROCdata scaling
AutoSolphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentUnited StatesNA19NOS4780181

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-08
    Type: Initial release
  • Version 1.1: 2020-05-20
    Changes: Database references
  • Version 1.2: 2020-06-10
    Changes: Database references
  • Version 1.3: 2020-06-17
    Changes: Database references
  • Version 1.4: 2024-03-06
    Changes: Data collection, Database references, Derived calculations, Refinement description