4RNQ | pdb_00004rnq

Crystal structure of tobacco 5-epi-aristolochene synthase (TEAS) with anilinogeranyl diphosphate (AGPP) and geraniline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 
    0.226 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Formation of a Novel Macrocyclic Alkaloid from the Unnatural Farnesyl Diphosphate Analogue Anilinogeranyl Diphosphate by 5-Epi-Aristolochene Synthase.

Rising, K.A.Crenshaw, C.M.Koo, H.J.Subramanian, T.Chehade, K.A.Starks, C.Allen, K.D.Andres, D.A.Spielmann, H.P.Noel, J.P.Chappell, J.

(2015) ACS Chem Biol 10: 1729-1736

  • DOI: https://doi.org/10.1021/acschembio.5b00145
  • Primary Citation Related Structures: 
    4RNQ

  • PubMed Abstract: 

    As part of an effort to identify substrate analogs suitable for helping to resolve structural features important for terpene synthases, the inhibition of 5-epi-aristolochene biosynthesis from farnesyl diphosphate (FPP) by the tobacco 5-epi-aristolochene synthase incubated with anilinogeranyl diphosphate (AGPP) was examined. The apparent noncompetitive nature of the inhibition supported further assessment of how AGPP might be bound to crystallographic forms of the enzyme. Surprisingly, the bound form of the inhibitor appeared to have undergone a cyclization event consistent with the native mechanism associated with FPP catalysis. Biocatalytic formation of a novel 13-membered macrocyclic paracyclophane alkaloid was confirmed by high-resolution GC-MS and NMR analysis. This work provides insights into new biosynthetic means for generating novel, functionally diversified, medium-sized terpene alkaloids.


  • Organizational Affiliation
    • †Departments of Pharmaceutical Sciences, ‡Cellular and Molecular Biochemistry, §Chemistry, ⊥Center for Structural Biology, ∥Markey Cancer Center, University of Kentucky, Lexington, Lexington, Kentucky, United States.

Macromolecule Content 

  • Total Structure Weight: 64.14 kDa 
  • Atom Count: 4,479 
  • Modeled Residue Count: 536 
  • Deposited Residue Count: 550 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
5-epi-aristolochene synthase550Nicotiana tabacumMutation(s): 0 
Gene Names: EAS3EAS4
EC: 4.2.3.61 (PDB Primary Data), 4.2.3.226 (UniProt), 4.2.3.227 (UniProt)
UniProt
Find proteins for Q40577 (Nicotiana tabacum)
Explore Q40577 
Go to UniProtKB:  Q40577
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ40577
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A4S

Query on A4S



Download:Ideal Coordinates CCD File
E [auth A](2E,6E)-3,7-dimethyl-8-(phenylamino)octa-2,6-dien-1-yl trihydrogen diphosphate
C16 H25 N O7 P2
HODAIPJPJAZJEY-GGQZXFEVSA-N
1GA

Query on 1GA



Download:Ideal Coordinates CCD File
F [auth A]Geraniline
C16 H21 N
QEYKICLOTYFCMW-QEKYNVLXSA-N
DPO

Query on DPO



Download:Ideal Coordinates CCD File
G [auth A]DIPHOSPHATE
O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-J
ACT

Query on ACT



Download:Ideal Coordinates CCD File
H [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free:  0.226 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.75α = 90
b = 126.75β = 90
c = 124.3γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
BOSdata collection
MOSFLMdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2015-07-29
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations