5YNW

Crystal structure of an aromatic prenyltransferase FAMD1 from Fischerella ambigua UTEX 1903 in complex with DMASPP and INN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Structural insight into a novel indole prenyltransferase in hapalindole-type alkaloid biosynthesis.

Wang, J.Chen, C.C.Yang, Y.Liu, W.Ko, T.P.Shang, N.Hu, X.Xie, Y.Huang, J.W.Zhang, Y.Guo, R.T.

(2018) Biochem Biophys Res Commun 495: 1782-1788

  • DOI: https://doi.org/10.1016/j.bbrc.2017.12.039
  • Primary Citation of Related Structures:  
    5YNT, 5YNU, 5YNV, 5YNW

  • PubMed Abstract: 

    FamD1 is a novel CloQ/NphB-family indole prenyltransferase which involves in hapalindole-type alkaloid biosynthesis. Here the native FamD1 structure and three protein-ligand complexes are analyzed to investigate the molecular basis of substrate binding and catalysis. FamD1 adopts a typical ABBA architecture of aromatic prenyltransferase, in which the substrate-binding chamber is found in the central β-barrel. The indole-containing acceptor substrate is bound adjacent to the prenyl donor. Based on the complex structures, a catalytic mechanism of FamD1 is proposed. Functional implications on the sister enzyme FamD2 are also discussed.


  • Organizational Affiliation

    Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
aromatic prenyltransferase
A, B
329Fischerella ambigua UTEX 1903Mutation(s): 0 
Gene Names: ambP3
EC: 2.5.1.159
UniProt
Find proteins for V5TDY7 (Fischerella ambigua (strain UTEX 1903))
Explore V5TDY7 
Go to UniProtKB:  V5TDY7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV5TDY7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DST
Query on DST

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
DIMETHYLALLYL S-THIOLODIPHOSPHATE
C5 H12 O6 P2 S
ZWFWSISPSBLNGO-UHFFFAOYSA-N
8XL
Query on 8XL

Download Ideal Coordinates CCD File 
E [auth B]3-[(Z)-2-isocyanoethenyl]-1H-indole
C11 H8 N2
JQMYMZZLIOIXEO-SREVYHEPSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD
Query on IMD

Download Ideal Coordinates CCD File 
G [auth B]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.583α = 90
b = 211.607β = 90
c = 82.421γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SOLVEphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2019-02-06
    Changes: Data collection, Structure summary
  • Version 2.0: 2019-10-16
    Changes: Data collection, Non-polymer description, Structure summary
  • Version 2.1: 2024-03-27
    Changes: Data collection, Database references, Structure summary