8FBC

Crystal structure of P450T2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Complete integration of carbene-transfer chemistry into biosynthesis.

Huang, J.Quest, A.Cruz-Morales, P.Deng, K.Pereira, J.H.Van Cura, D.Kakumanu, R.Baidoo, E.E.K.Dan, Q.Chen, Y.Petzold, C.J.Northen, T.R.Adams, P.D.Clark, D.S.Balskus, E.P.Hartwig, J.F.Mukhopadhyay, A.Keasling, J.D.

(2023) Nature 617: 403-408

  • DOI: https://doi.org/10.1038/s41586-023-06027-2
  • Primary Citation of Related Structures:  
    8FBC

  • PubMed Abstract: 

    Biosynthesis is an environmentally benign and renewable approach that can be used to produce a broad range of natural and, in some cases, new-to-nature products. However, biology lacks many of the reactions that are available to synthetic chemists, resulting in a narrower scope of accessible products when using biosynthesis rather than synthetic chemistry. A prime example of such chemistry is carbene-transfer reactions 1 . Although it was recently shown that carbene-transfer reactions can be performed in a cell and used for biosynthesis 2,3 , carbene donors and unnatural cofactors needed to be added exogenously and transported into cells to effect the desired reactions, precluding cost-effective scale-up of the biosynthesis process with these reactions. Here we report the access to a diazo ester carbene precursor by cellular metabolism and a microbial platform for introducing unnatural carbene-transfer reactions into biosynthesis. The α-diazoester azaserine was produced by expressing a biosynthetic gene cluster in Streptomyces albus. The intracellularly produced azaserine was used as a carbene donor to cyclopropanate another intracellularly produced molecule-styrene. The reaction was catalysed by engineered P450 mutants containing a native cofactor with excellent diastereoselectivity and a moderate yield. Our study establishes a scalable, microbial platform for conducting intracellular abiological carbene-transfer reactions to functionalize a range of natural and new-to-nature products and expands the scope of organic products that can be produced by cellular metabolism.


  • Organizational Affiliation

    Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450
A, B
395metagenomeMutation(s): 0 
Gene Names: DCM06_12860
UniProt
Find proteins for A0A3C0KFZ6 (Comamonadaceae bacterium)
Explore A0A3C0KFZ6 
Go to UniProtKB:  A0A3C0KFZ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3C0KFZ6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.931α = 90
b = 95.61β = 90
c = 100.433γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
xia2data reduction
xia2data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-AC02-05CH11231

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-10
    Type: Initial release
  • Version 1.1: 2023-05-17
    Changes: Database references