8JOO

Crystal structure of cytochrome P450 IkaD from Streptomyces sp. ZJ306, in complex with the substrate ikarugamycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

Starting Model: experimental
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Literature

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 62: 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

    Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, 510301, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450
A, B
408Streptomyces sp. ZJ306Mutation(s): 0 
UniProt
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
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
EIA (Subject of Investigation/LOI)
Query on EIA

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
(1Z,3E,5S,7R,8R,10R,11R,12S,15R,16S,18Z,25S)-11-ethyl-2-hydroxy-10-methyl-21,26-diazapentacyclo[23.2.1.05,16.07,15.08,12]octacosa-1(2),3,13,18-tetraene-20,27,28-trione
C29 H38 N2 O4
GHXZHWYUSAWISC-KZRBWAKNSA-N
FMT
Query on FMT

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
J [auth B]
K [auth B]
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B],
L [auth B]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
M [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.174α = 90
b = 82.121β = 94.41
c = 143.92γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
CrysalisProdata reduction
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China22177118
National Natural Science Foundation of China (NSFC)China31630004

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-15
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Database references