9S7F | pdb_00009s7f

Crystal structure of DoxA in complex with substrate DOD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 
    0.222 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.200 (DCC) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Metabolic engineering of doxorubicin biosynthesis through P450-redox partner optimization and structural analysis of DoxA.

Koroleva, A.Artukka, E.Yamada, K.Newmister, S.A.Harte, R.J.Boesger, H.Londen, M.Sanders, J.N.Tirkkonen, H.Kannisto, M.Kuin, R.C.M.Hulst, M.Wang, R.Leskinen, E.Barillec, M.Niemi, J.van Wezel, G.P.Neefjes, J.Nybo, S.E.Houk, K.N.Sherman, D.H.Kim, R.Q.Metsa-Ketela, M.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-69194-6
  • Primary Citation Related Structures: 
    9O35, 9S7F, 9SI5

  • PubMed Abstract: 

    Doxorubicin, a widely used chemotherapy drug, is produced by Streptomyces peucetius ATCC27952. The biosynthesis relies on the cytochrome P450 monooxygenase DoxA, which catalyzes three consecutive late-stage oxidation steps. However, conversion from daunorubicin to doxorubicin is inefficient, necessitating semi-synthetic industrial manufacturing. Here, we address key limitations in DoxA catalysis. We identify the natural redox partners ferredoxin Fdx4 and ferredoxin reductase FdR3 by transcriptomic analysis. We discovered the vicinal oxygen chelate family protein DnrV to prevent product inhibition by binding doxorubicin. Structural analysis of DoxA and density functional theory (DFT) calculations reveal that inefficient C14 hydroxylation results from the unfavorable anti-conformation of the methyl ketone side chain of daunorubicin. We harness these advances for rational strain engineering, leading to an 180% increase in doxorubicin yields and an improved production profile. This study provides singular insights into enzymatic constraints in anthracycline biosynthesis and facilitates cost-effective manufacturing to meet the growing global demand for doxorubicin.


  • Organizational Affiliation
    • Department of Life Technologies, University of Turku, Turku, Finland.

Macromolecule Content 

  • Total Structure Weight: 101.66 kDa 
  • Atom Count: 6,775 
  • Modeled Residue Count: 812 
  • Deposited Residue Count: 914 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome P-450 monooxygenase DoxAA,
B [auth D]
457Streptomyces peucetiusMutation(s): 0 
Gene Names: doxA
EC: 1.14.13.181
UniProt
Find proteins for Q9ZAU3 (Streptomyces peucetius)
Explore Q9ZAU3 
Go to UniProtKB:  Q9ZAU3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZAU3
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free:  0.222 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.200 (DCC) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.755α = 90
b = 107.708β = 90
c = 184.457γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-24
    Type: Initial release
  • Version 1.1: 2026-02-18
    Changes: Database references
  • Version 1.2: 2026-03-25
    Changes: Database references