8JNP | pdb_00008jnp

Crystal structure of cytochrome P450 CftA from Streptomyces torulosus NRRL B-3889, in complex with the substrate ikarugamycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.237 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

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 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.

Macromolecule Content 

  • Total Structure Weight: 45.18 kDa 
  • Atom Count: 3,513 
  • Modeled Residue Count: 390 
  • Deposited Residue Count: 396 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome P450 CftA396Streptomyces torulosusMutation(s): 0 
UniProt
Find proteins for A0AAJ6N6I0 (Streptomyces torulosus)
Explore A0AAJ6N6I0 
Go to UniProtKB:  A0AAJ6N6I0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AAJ6N6I0
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
(Subject of Investigation/LOI)

Query on HEM



Download:Ideal Coordinates CCD File
C [auth A]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
B [auth A](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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.237 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.197α = 90
b = 68.383β = 90
c = 108.795γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
CrysalisProdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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