3O2K | pdb_00003o2k

Crystal Structure of Brevianamide F Prenyltransferase Complexed with Brevianamide F and Dimethylallyl S-thiolodiphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.235 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

Structure-function analysis of an enzymatic prenyl transfer reaction identifies a reaction chamber with modifiable specificity.

Jost, M.Zocher, G.Tarcz, S.Matuschek, M.Xie, X.Li, S.M.Stehle, T.

(2010) J Am Chem Soc 132: 17849-17858

  • DOI: https://doi.org/10.1021/ja106817c
  • Primary Citation Related Structures: 
    3O24, 3O2K

  • PubMed Abstract: 

    Fungal indole prenyltransferases participate in a multitude of biosynthetic pathways. Their ability to prenylate diverse substrates has attracted interest for potential use in chemoenzymatic synthesis. The fungal indole prenyltransferase FtmPT1 catalyzes the prenylation of brevianamide F in the biosynthesis of fumitremorgin-type alkaloids, which show diverse pharmacological activities and are promising candidates for the development of antitumor agents. Here, we report crystal structures of unliganded Aspergillus fumigatus FtmPT1 as well as of a ternary complex of FtmPT1 bound to brevianamide F and an analogue of its isoprenoid substrate dimethylallyl diphosphate. FtmPT1 assumes a rare α/β-barrel fold, consisting of 10 circularly arranged β-strands surrounded by α-helices. Catalysis is performed in a hydrophobic reaction chamber at the center of the barrel. In combination with mutagenesis experiments, our analysis of the liganded and unliganded structures provides insight into the mechanism of catalysis and the determinants of regiospecificity. Sequence conservation of key features indicates that all fungal indole prenyltransferases possess similar active site architectures. However, while the dimethylallyl diphosphate binding site is strictly conserved in these enzymes, subtle changes in the reaction chamber likely allow for the accommodation of diverse aromatic substrates for prenylation. In support of this concept, we were able to redirect the regioselectivity of FtmPT1 by a single mutation of glycine 115 to threonine. This finding provides support for a potential use of fungal indole prenyltransferases as modifiable bioreactors that can be engineered to catalyze highly specific prenyl transfer reactions.


  • Organizational Affiliation
    • Interfakultäres Institut für Biochemie, Universität Tübingen, Hoppe-Seyler-Strasse 4, 72076 Tübingen, Germany.

Macromolecule Content 

  • Total Structure Weight: 54.71 kDa 
  • Atom Count: 3,488 
  • Modeled Residue Count: 429 
  • Deposited Residue Count: 474 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Brevianamide F prenyltransferase474Aspergillus fumigatusMutation(s): 0 
Gene Names: ftmPT1
EC: 3.4.11.17 (UniProt), 2.5.1.106 (UniProt)
UniProt
Find proteins for Q4WAW7 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293))
Explore Q4WAW7 
Go to UniProtKB:  Q4WAW7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4WAW7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QRP

Query on QRP



Download:Ideal Coordinates CCD File
C [auth A](3S,8aS)-3-(1H-indol-3-ylmethyl)hexahydropyrrolo[1,2-a]pyrazine-1,4-dione
C16 H17 N3 O2
RYFZBPVMVYTEKZ-KBPBESRZSA-N
DST

Query on DST



Download:Ideal Coordinates CCD File
B [auth A]DIMETHYLALLYL S-THIOLODIPHOSPHATE
C5 H12 O6 P2 S
ZWFWSISPSBLNGO-UHFFFAOYSA-N
MES

Query on MES



Download:Ideal Coordinates CCD File
D [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.235 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.77α = 90
b = 82.77β = 90
c = 124.26γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2019-10-02
    Changes: Data collection, Non-polymer description, Structure summary
  • Version 2.1: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary