6VYA

Crystal structure of NotF in complex with brevianamide F and DMSPP

  • Classification: TRANSFERASE
  • Organism(s): Aspergillus sp. MF297-2
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2020-02-25 Released: 2021-02-03 
  • Deposition Author(s): Dan, Q., Smith, J.L.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.265 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Data Science-Driven Analysis of Substrate-Permissive Diketopiperazine Reverse Prenyltransferase NotF: Applications in Protein Engineering and Cascade Biocatalytic Synthesis of (-)-Eurotiumin A.

Kelly, S.P.Shende, V.V.Flynn, A.R.Dan, Q.Ye, Y.Smith, J.L.Tsukamoto, S.Sigman, M.S.Sherman, D.H.

(2022) J Am Chem Soc 144: 19326-19336

  • DOI: https://doi.org/10.1021/jacs.2c06631
  • Primary Citation of Related Structures:  
    6VY9, 6VYA

  • PubMed Abstract: 

    Prenyltransfer is an early-stage carbon-hydrogen bond (C-H) functionalization prevalent in the biosynthesis of a diverse array of biologically active bacterial, fungal, plant, and metazoan diketopiperazine (DKP) alkaloids. Toward the development of a unified strategy for biocatalytic construction of prenylated DKP indole alkaloids, we sought to identify and characterize a substrate-permissive C2 reverse prenyltransferase (PT). As the first tailoring event within the biosynthesis of cytotoxic notoamide metabolites, PT NotF catalyzes C2 reverse prenyltransfer of brevianamide F. Solving a crystal structure of NotF (in complex with native substrate and prenyl donor mimic dimethylallyl S-thiolodiphosphate (DMSPP)) revealed a large, solvent-exposed active site, intimating NotF may possess a significantly broad substrate scope. To assess the substrate selectivity of NotF, we synthesized a panel of 30 sterically and electronically differentiated tryptophanyl DKPs, the majority of which were selectively prenylated by NotF in synthetically useful conversions (2 to >99%). Quantitative representation of this substrate library and development of a descriptive statistical model provided insight into the molecular origins of NotF's substrate promiscuity. This approach enabled the identification of key substrate descriptors (electrophilicity, size, and flexibility) that govern the rate of NotF-catalyzed prenyltransfer, and the development of an "induced fit docking (IFD)-guided" engineering strategy for improved turnover of our largest substrates. We further demonstrated the utility of NotF in tandem with oxidative cyclization using flavin monooxygenase, BvnB. This one-pot, in vitro biocatalytic cascade enabled the first chemoenzymatic synthesis of the marine fungal natural product, (-)-eurotiumin A, in three steps and 60% overall yield.


  • Organizational Affiliation

    Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Deoxybrevianamide E synthase notF472Aspergillus sp. MF297-2Mutation(s): 0 
Gene Names: notF
EC: 2.5.1.109
UniProt
Find proteins for E0Y3X1 (Aspergillus sp. (strain MF297-2))
Explore E0Y3X1 
Go to UniProtKB:  E0Y3X1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE0Y3X1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QRP (Subject of Investigation/LOI)
Query on QRP

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth N]
CA [auth V]
CB [auth O]
EA [auth E]
AA [auth A],
AB [auth N],
CA [auth V],
CB [auth O],
EA [auth E],
EB [auth P],
GA [auth G],
GB [auth Q],
IA [auth B],
IB [auth R],
KA [auth D],
KB [auth S],
MA [auth F],
MB [auth T],
OA [auth H],
OB [auth U],
QA [auth I],
QB [auth W],
SA [auth J],
SB [auth X],
UA [auth K],
WA [auth L],
Y [auth C],
YA [auth M]
(3S,8aS)-3-(1H-indol-3-ylmethyl)hexahydropyrrolo[1,2-a]pyrazine-1,4-dione
C16 H17 N3 O2
RYFZBPVMVYTEKZ-KBPBESRZSA-N
DST (Subject of Investigation/LOI)
Query on DST

Download Ideal Coordinates CCD File 
BA [auth A]
BB [auth N]
DA [auth V]
DB [auth O]
FA [auth E]
BA [auth A],
BB [auth N],
DA [auth V],
DB [auth O],
FA [auth E],
FB [auth P],
HA [auth G],
HB [auth Q],
JA [auth B],
JB [auth R],
LA [auth D],
LB [auth S],
NA [auth F],
NB [auth T],
PA [auth H],
PB [auth U],
RA [auth I],
RB [auth W],
TA [auth J],
TB [auth X],
VA [auth K],
XA [auth L],
Z [auth C],
ZA [auth M]
DIMETHYLALLYL S-THIOLODIPHOSPHATE
C5 H12 O6 P2 S
ZWFWSISPSBLNGO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.265 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.893α = 78.255
b = 163.069β = 65.051
c = 167.857γ = 66.396
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesDK042303

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-03
    Type: Initial release
  • Version 1.1: 2023-03-01
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description