5YNW | pdb_00005ynw

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

• PDB DOI: https://doi.org/10.2210/pdb5YNW/pdb

• Classification: TRANSFERASE
• Organism(s): Fischerella ambigua UTEX 1903
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-10-25 Released: 2018-08-29 
• Deposition Author(s): Wang, J., Liu, W.D., Chen, C.C., Guo, R.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.194 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

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

• PubMed: 29229390 
• DOI: https://doi.org/10.1016/j.bbrc.2017.12.039
• Primary Citation 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.

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Organizational Affiliation: 
• Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China.
Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan.
Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; School of Biotechnology, Jiangnan University, Wuxi 214122, China.
School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China. Electronic address: [e-mail].
Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 74.83 kDa 
• Atom Count: 5,498 
• Modeled Residue Count: 613 
• Deposited Residue Count: 658 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
aromatic prenyltransferase	A, B	329	Fischerella ambigua UTEX 1903	Mutation(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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DST	C [auth A], F [auth B]	DIMETHYLALLYL S-THIOLODIPHOSPHATE C5 H12 O6 P2 S ZWFWSISPSBLNGO-UHFFFAOYSA-N
8XL	E [auth B]	3-[(Z)-2-isocyanoethenyl]-1H-indole C11 H8 N2 JQMYMZZLIOIXEO-SREVYHEPSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD	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 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.583	α = 90
b = 211.607	β = 90
c = 82.421	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-29 
Deposition Author(s): Wang, J., Liu, W.D., Chen, C.C., Guo, R.T.

Revision History  

• 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