5KD6

Crystal structure of the aromatic prenyltransferase AtaPT from Aspergillus terreus A8-4 in complex with dimethylallyl S-thiolodiphosphate and (-)-butyrolactone II

  • Classification: TRANSFERASE
  • Organism(s): Aspergillus terreus
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2016-06-07 Released: 2016-12-21 
  • Deposition Author(s): Sun, F., Gao, B.
  • Funding Organization(s): Chinese Academy of Sciences, Ministry of Science and Technology of China, National Natural Science Foundation of China

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Molecular insights into the enzyme promiscuity of an aromatic prenyltransferase.

Chen, R.Gao, B.Liu, X.Ruan, F.Zhang, Y.Lou, J.Feng, K.Wunsch, C.Li, S.M.Dai, J.Sun, F.

(2017) Nat Chem Biol 13: 226-234

  • DOI: https://doi.org/10.1038/nchembio.2263
  • Primary Citation of Related Structures:  
    5KCG, 5KCL, 5KCQ, 5KCY, 5KD0, 5KD6, 5KDA

  • PubMed Abstract: 

    Aromatic prenyltransferases (aPTases) transfer prenyl moieties from isoprenoid donors to various aromatic acceptors, some of which have the rare property of extreme enzymatic promiscuity toward both a variety of prenyl donors and a large diversity of acceptors. In this study, we discovered a new aPTase, AtaPT, from Aspergillus terreus that exhibits unprecedented promiscuity toward diverse aromatic acceptors and prenyl donors and also yields products with a range of prenylation patterns. Systematic crystallographic studies revealed various discrete conformations for ligand binding with donor-dependent acceptor specificity and multiple binding sites within a spacious hydrophobic substrate-binding pocket. Further structure-guided mutagenesis of active sites at the substrate-binding pocket is responsible for altering the specificity and promiscuity toward substrates and the diversity of product prenylations. Our study reveals the molecular mechanism underlying the promiscuity of AtaPT and suggests an efficient protein engineering strategy to generate new prenylated derivatives in drug discovery applications.


  • Organizational Affiliation

    State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
aromatic prenyltransferase
A, B
419Aspergillus terreusMutation(s): 0 
UniProt
Find proteins for A0A1B0UHJ4 (Aspergillus terreus)
Explore A0A1B0UHJ4 
Go to UniProtKB:  A0A1B0UHJ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1B0UHJ4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LBU
Query on LBU

Download Ideal Coordinates CCD File 
D [auth B]methyl (2S)-4-hydroxy-3-(4-hydroxyphenyl)-2-[(4-hydroxyphenyl)methyl]-5-oxo-2,5-dihydrofuran-2-carboxylate
C19 H16 O7
AEKPZNDJHWFONI-IBGZPJMESA-N
DST
Query on DST

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
DIMETHYLALLYL S-THIOLODIPHOSPHATE
C5 H12 O6 P2 S
ZWFWSISPSBLNGO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.06α = 90
b = 134.14β = 90
c = 68.62γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaXDB08030202
Ministry of Science and Technology of ChinaChina2014CB910700
National Natural Science Foundation of ChinaChina81302667

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2017-07-05
    Changes: Database references
  • Version 2.0: 2019-10-16
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Refinement description, Structure summary
  • Version 2.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary