8FBC | pdb_00008fbc

Crystal structure of P450T2

PDB DOI: https://doi.org/10.2210/pdb8FBC/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): metagenome
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-11-29 Released: 2023-05-10
Deposition Author(s): Pereira, J.H., Huang, J., Keasling, J., Adams, P.D.
Funding Organization(s): Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free:
0.191 (Depositor), 0.191 (DCC)
R-Value Work:
0.164 (Depositor), 0.164 (DCC)
R-Value Observed:
0.165 (Depositor)

Starting Model: in silico
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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

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

PubMed: 37138074 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41586-023-06027-2
Primary Citation 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.

Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA.

Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA.

Department of Chemistry, University of California, Berkeley, CA, USA.

Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.

Department of Biomaterials and Biomanufacturing, Sandia National Laboratories, Livermore, CA, USA.

Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.

Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

Department of Bioengineering, University of California, Berkeley, CA, USA.

Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA. dsc@berkeley.edu.

Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. dsc@berkeley.edu.

Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.

Department of Chemistry, University of California, Berkeley, CA, USA. jhartwig@berkeley.edu.

Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. jhartwig@berkeley.edu.

Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. amukhopadhyay@lbl.gov.

Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA. amukhopadhyay@lbl.gov.

Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. amukhopadhyay@lbl.gov.

Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. keasling@berkeley.edu.

Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA. keasling@berkeley.edu.

Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA. keasling@berkeley.edu.

Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark. keasling@berkeley.edu.

Department of Bioengineering, University of California, Berkeley, CA, USA. keasling@berkeley.edu.

Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China. keasling@berkeley.edu.

Macromolecule Content

Total Structure Weight: 89.86 kDa
Atom Count: 7,309
Modeled Residue Count: 784
Deposited Residue Count: 790
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450	A, B	395	metagenome	Mutation(s): 0 Gene Names: DCM06_12860

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]