4KVD

Crystal structure of Aspergillus terreus aristolochene synthase complexed with (4aS,7S)-1,4a-dimethyl-7-(prop-1-en-2-yl)decahydroquinolin-1-ium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Mechanistic insights from the binding of substrate and carbocation intermediate analogues to aristolochene synthase.

Chen, M.Al-Lami, N.Janvier, M.D'Antonio, E.L.Faraldos, J.A.Cane, D.E.Allemann, R.K.Christianson, D.W.

(2013) Biochemistry 52: 5441-5453

  • DOI: https://doi.org/10.1021/bi400691v
  • Primary Citation of Related Structures:  
    4KUX, 4KVD, 4KVI, 4KVW, 4KVY, 4KWD

  • PubMed Abstract: 

    Aristolochene synthase, a metal-dependent sesquiterpene cyclase from Aspergillus terreus, catalyzes the ionization-dependent cyclization of farnesyl diphosphate (FPP) to form the bicyclic eremophilane (+)-aristolochene with perfect structural and stereochemical precision. Here, we report the X-ray crystal structure of aristolochene synthase complexed with three Mg(2+) ions and the unreactive substrate analogue farnesyl-S-thiolodiphosphate (FSPP), showing that the substrate diphosphate group is anchored by metal coordination and hydrogen bond interactions identical to those previously observed in the complex with three Mg(2+) ions and inorganic pyrophosphate (PPi). Moreover, the binding conformation of FSPP directly mimics that expected for productively bound FPP, with the exception of the precise alignment of the C-S bond with regard to the C10-C11 π system that would be required for C1-C10 bond formation in the first step of catalysis. We also report crystal structures of aristolochene synthase complexed with Mg(2+)3-PPi and ammonium or iminium analogues of bicyclic carbocation intermediates proposed for the natural cyclization cascade. Various binding orientations are observed for these bicyclic analogues, and these orientations appear to be driven by favorable electrostatic interactions between the positively charged ammonium group of the analogue and the negatively charged PPi anion. Surprisingly, the active site is sufficiently flexible to accommodate analogues with partially or completely incorrect stereochemistry. Although this permissiveness in binding is unanticipated, based on the stereochemical precision of catalysis that leads exclusively to the (+)-aristolochene stereoisomer, it suggests the ability of the active site to enable controlled reorientation of intermediates during the cyclization cascade. Taken together, these structures illuminate important aspects of the catalytic mechanism.


  • Organizational Affiliation

    Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aristolochene synthase
A, B, C, D
314Aspergillus terreusMutation(s): 0 
Gene Names: Ari1
EC: 4.2.3.9
UniProt
Find proteins for Q9UR08 (Aspergillus terreus)
Explore Q9UR08 
Go to UniProtKB:  Q9UR08
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UR08
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1SS
Query on 1SS

Download Ideal Coordinates CCD File 
CA [auth D],
L [auth A],
M [auth B],
X [auth C]
(1R,4aS,7S,8aR)-1,4a-dimethyl-7-(prop-1-en-2-yl)decahydroquinolinium
C14 H26 N
HQXXDILNZLFDML-BFHYXJOUSA-O
POP
Query on POP

Download Ideal Coordinates CCD File 
E [auth A],
N [auth B],
S [auth C],
Y [auth D]
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
R [auth B],
W [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
F [auth A]
G [auth A]
H [auth A]
AA [auth D],
BA [auth D],
F [auth A],
G [auth A],
H [auth A],
K [auth A],
O [auth B],
P [auth B],
Q [auth B],
T [auth C],
U [auth C],
V [auth C],
Z [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.788α = 90
b = 122.788β = 90
c = 202.532γ = 120
Software Package:
Software NamePurpose
CBASSdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-14
    Type: Initial release
  • Version 1.1: 2013-08-28
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description