Multifunctional cytochrome P450 enzyme IkaD from Streptomyces sp. ZJ306, in complex with epoxyikarugamycin

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report

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A Mechanistic Understanding of the Distinct Regio- and Chemoselectivity of Multifunctional P450s by Structural Comparison of IkaD and CftA Complexed with Common Substrates.

Jiang, P.Jin, H.Zhang, G.Zhang, W.Liu, W.Zhu, Y.Zhang, C.Zhang, L.

(2023) Angew Chem Int Ed Engl : e202310728-e202310728

  • DOI: https://doi.org/10.1002/anie.202310728
  • Primary Citation of Related Structures:  
    8JNC, 8JNO, 8JNP, 8JNQ, 8JOO, 8JUA

  • PubMed Abstract: 

    Regio- and chemoselective C-H activation at multi-positions of a single molecule is fascinating but chemically challenging. The homologous cytochrome P450 enzymes IkaD and CftA catalyze multiple C-H oxidations on the same polycyclic tetramate macrolactam (PoTeM) ikarugamycin, with distinct regio- and chemoselectivity. Herein we provide mechanistic understanding of their functional differences by solving crystal structures of IkaD and CftA in complex with ikarugamycin and unnatural substrates. Distinct conformations of the F/G region in IkaD and CftA are found to differentiate the orientation of PoTeM substrates, by causing different binding patterns with polar moieties to determine site selection, oxidation order, and chemoselectivity. Fine-tuning the polar subpocket altered the regioselectivity of IkaD, indicating that substrate re-orientation by mutating residues distal to the oxidation site could serve as an important method in future engineering of P450 enzymes.

  • Organizational Affiliation

    University of Chinese Academy of Science, 19 Yuquan Road, Beijing, 100049, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450
A, B
428Streptomyces sp. ZJ306Mutation(s): 0 
Find proteins for A0A0B4ZV78 (Streptomyces sp. ZJ306)
Explore A0A0B4ZV78 
Go to UniProtKB:  A0A0B4ZV78
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0B4ZV78
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
K [auth B]
C34 H32 Fe N4 O4
F7Z (Subject of Investigation/LOI)
Query on F7Z

Download Ideal Coordinates CCD File 
D [auth A],
L [auth B]
(1Z,3E,5S,7R,8R,10R,11R,12S,13R,15S,16R,17S,19Z,26S)-11-ethyl-2-hydroxy-10-methyl-22,27-diaza-14 oxahexacyclo[,17.07,16.013,15.08,12]nonacosa-1(2),3,19-triene-21,28,29-trione
C29 H38 N2 O5
Query on FMT

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
M [auth B],
N [auth B]
C H2 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.6201α = 90
b = 81.9395β = 94.3858
c = 144.165γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
CrysalisProdata reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China22193072
National Natural Science Foundation of China (NSFC)China22177118

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-15
    Type: Initial release