5VWS

Ligand free structure of Cytochrome P450 TbtJ1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.411 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

P450-Mediated Non-natural Cyclopropanation of Dehydroalanine-Containing Thiopeptides.

Gober, J.G.Ghodge, S.V.Bogart, J.W.Wever, W.J.Watkins, R.R.Brustad, E.M.Bowers, A.A.

(2017) ACS Chem. Biol. 12: 1726-1731

  • DOI: 10.1021/acschembio.7b00358

  • PubMed Abstract: 
  • Thiopeptides are a growing class of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products. Many biosynthetic enzymes for RiPPs, especially thiopeptides, are promiscuous and can accept a wide range of peptide substr ...

    Thiopeptides are a growing class of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products. Many biosynthetic enzymes for RiPPs, especially thiopeptides, are promiscuous and can accept a wide range of peptide substrates with different amino acid sequences; thus, these enzymes have been used as tools to generate new natural product derivatives. Here, we explore an alternative route to molecular complexity by engineering thiopeptide tailoring enzymes to do new or non-native chemistry. We explore cytochrome P450 enzymes as biocatalysts for cyclopropanation of dehydroalanines, chemical motifs found widely in thiopeptides and other RiPP-based natural products. We find that P450TbtJ1 and P450TbtJ2 selectively cyclopropanate dehydroalanines in a number of complex thiopeptide-based substrates and convert them into 1-amino-2-cyclopropane carboxylic acids (ACCAs), which are important pharmacophores. This chemistry takes advantage of the innate affinity of these biosynthetic enzymes for their substrates and enables incorporation of new pharmacophores into thiopeptide architectures. This work also presents a strategy for diversification of natural products through rationally repurposing biosynthetic enzymes as non-natural biocatalysts.


    Organizational Affiliation

    Department of Chemistry, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27514, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome P450
A
393Thermobispora bispora (strain ATCC 19993 / DSM 43833 / CBS 139.67 / JCM 10125 / NBRC 14880 / R51)Mutation(s): 0 
Find proteins for D6Y4Z8 (Thermobispora bispora (strain ATCC 19993 / DSM 43833 / CBS 139.67 / JCM 10125 / NBRC 14880 / R51))
Go to UniProtKB:  D6Y4Z8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.411 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.208 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 95.316α = 90.00
b = 95.316β = 90.00
c = 126.782γ = 90.00
Software Package:
Software NamePurpose
KYLINdata scaling
PHENIXphasing
PHENIXrefinement
KYLINdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (United States)United StatesCHE-1552718
Beckman InstituteUnited States--
National Institutes of Health/National Cancer InstituteUnited StatesP30CA016086

Revision History 

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-08-02
    Type: Author supporting evidence, Database references
  • Version 1.2: 2017-08-23
    Type: Data collection