5DHK

Nicotiana tabacum 5-epi-aristolochene synthase mutant W273E - alkylated

  • Classification: LYASE
  • Organism(s): Nicotiana tabacum
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): 

  • Deposited: 2015-08-31 Released: 2015-09-16 
  • Deposition Author(s): Noel, J.P., Kersten, R.K.
  • Funding Organization(s): National Science Foundation (United States); National Institutes of Health/National Institute of General Medical Sciences 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Mechanism-Based Post-Translational Modification and Inactivation in Terpene Synthases.

Kersten, R.D.Diedrich, J.K.Yates, J.R.Noel, J.P.

(2015) Acs Chem.Biol. 10: 2501-2511

  • DOI: 10.1021/acschembio.5b00539
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Terpenes are ubiquitous natural chemicals with diverse biological functions spanning all three domains of life. In specialized metabolism, the active sites of terpene synthases (TPSs) evolve in shape and reactivity to direct the biosynthesis of a myr ...

    Terpenes are ubiquitous natural chemicals with diverse biological functions spanning all three domains of life. In specialized metabolism, the active sites of terpene synthases (TPSs) evolve in shape and reactivity to direct the biosynthesis of a myriad of chemotypes for organismal fitness. As most terpene biosynthesis mechanistically involves highly reactive carbocationic intermediates, the protein surfaces catalyzing these cascade reactions possess reactive regions possibly prone to premature carbocation capture and potentially enzyme inactivation. Here, we show using proteomic and X-ray crystallographic analyses that cationic intermediates undergo capture by conserved active site residues leading to inhibitory self-alkylation. Moreover, the level of cation-mediated inactivation increases with mutation of the active site, upon changes in the size and structure of isoprenoid diphosphate substrates, and alongside increases in reaction temperatures. TPSs that individually synthesize multiple products are less prone to self-alkylation then TPSs possessing relatively high product specificity. In total, the results presented suggest that mechanism-based alkylation represents an overlooked mechanistic pressure during the evolution of cation-derived terpene biosynthesis.


    Organizational Affiliation

    Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology & Proteomics, The Salk Institute for Biological Studies , La Jolla, California 92037, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5-epi-aristolochene synthase
A
536Nicotiana tabacumMutation(s): 1 
Gene Names: EAS3, EAS4
EC: 4.2.3.61
Find proteins for Q40577 (Nicotiana tabacum)
Go to UniProtKB:  Q40577
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAR
Query on FAR

Download SDF File 
Download CCD File 
A
FARNESYL
C15 H26
JXBSHSBNOVLGHF-BUJBXKITSA-N
 Ligand Interaction
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: 2.43 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.194 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 126.690α = 90.00
b = 126.690β = 90.00
c = 122.000γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXphasing
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (United States)United StatesEEC-0813570
National Institutes of Health/National Institute of General Medical SciencesUnited States8 P41 GM103533

Revision History 

  • Version 1.0: 2015-09-16
    Type: Initial release
  • Version 1.1: 2015-09-30
    Type: Database references
  • Version 1.2: 2015-12-02
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Derived calculations