Crystal structure of cytochrome P450 Sas16 from Streptomyces asterosporus

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

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P450-mediated dehydrotyrosine formation during WS9326 biosynthesis proceeds via dehydrogenation of a specific acylated dipeptide substrate.

Zhang, S.Zhang, L.Greule, A.Tailhades, J.Marschall, E.Prasongpholchai, P.Leng, D.J.Zhang, J.Zhu, J.Kaczmarski, J.A.Schittenhelm, R.B.Einsle, O.Jackson, C.J.Alberti, F.Bechthold, A.Zhang, Y.Tosin, M.Si, T.Cryle, M.J.

(2023) Acta Pharm Sin B 13: 3561-3574

  • DOI: https://doi.org/10.1016/j.apsb.2023.03.021
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    WS9326A is a peptide antibiotic containing a highly unusual N -methyl- E -2-3-dehydrotyrosine (NMet-Dht) residue that is incorporated during peptide assembly on a non-ribosomal peptide synthetase (NRPS). The cytochrome P450 encoded by sas16 (P450 Sas ) has been shown to be essential for the formation of the alkene moiety in NMet-Dht, but the timing and mechanism of the P450 Sas -mediated α , β -dehydrogenation of Dht remained unclear. Here, we show that the substrate of P450 Sas is the NRPS-associated peptidyl carrier protein (PCP)-bound dipeptide intermediate ( Z )-2-pent-1'-enyl-cinnamoyl-Thr- N -Me-Tyr. We demonstrate that P450 Sas -mediated incorporation of the double bond follows N -methylation of the Tyr by the N- methyl transferase domain found within the NRPS, and further that P450 Sas appears to be specific for substrates containing the ( Z )-2-pent-1'-enyl-cinnamoyl group. A crystal structure of P450 Sas reveals differences between P450 Sas and other P450s involved in the modification of NRPS-associated substrates, including the substitution of the canonical active site alcohol residue with a phenylalanine (F250), which in turn is critical to P450 Sas activity and WS9326A biosynthesis. Together, our results suggest that P450 Sas catalyses the direct dehydrogenation of the NRPS-bound dipeptide substrate, thus expanding the repertoire of P450 enzymes that can be used to produce biologically active peptides.

  • Organizational Affiliation

    CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450
A, B
443Streptomyces calvusMutation(s): 0 
Gene Names: CD934_23940
Find proteins for A0A0N9M5Z3 (Streptomyces calvus)
Explore A0A0N9M5Z3 
Go to UniProtKB:  A0A0N9M5Z3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0N9M5Z3
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.838α = 90
b = 112.838β = 90
c = 146.182γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyRTG1976

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-22
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references