8ZZD | pdb_00008zzd

Integrative structure of P450-Ferredoxin Complex

Integrative structure models are generated using different types of input information, including varied experimental data, physical principles, statistical preferences, and other prior information.


Integrative Structure Snapshot

  • Multi-Scale: No 
  • Multi-State: No 
  • Ordered-State: No 
  • Deposited Models: 
  • Representative Model: 

This is version 1.0 of the entry. See complete history

Literature

A Structural Model of a P450-Ferredoxin Complex from Orientation-Selective Double Electron-Electron Resonance Spectroscopy

Bowen, A.M.Johnson, E.O.D.Mercuri, F.Hoskins, N.J.Qiao, R.McCullagh, J.S.O.Lovett, J.E.Bell, S.G.Zhou, W.Timmel, C.R.Wong, L.L.Harmer, J.H.

(2018) J Am Chem Soc 140: 2514-2527

  • DOI: https://doi.org/10.1021/jacs.7b11056
  • Primary Citation Related Structures: 
    8ZZD

  • PubMed Abstract: 

    Cytochrome P450 (CYP) monooxygenases catalyze the oxidation of chemically inert carbon-hydrogen bonds in diverse endogenous and exogenous organic compounds by atmospheric oxygen. This C-H bond oxy-functionalization activity has huge potential in biotechnological applications. Class I CYPs receive the two electrons required for oxygen activation from NAD(P)H via a ferredoxin reductase and ferredoxin. The interaction of Class I CYPs with their cognate ferredoxin is specific. In order to reconstitute the activity of diverse CYPs, structural characterization of CYP-ferredoxin complexes is necessary, but little structural information is available. Here we report a structural model of such a complex (CYP199A2-HaPux) in frozen solution derived from distance and orientation restraints gathered by the EPR technique of orientation-selective double electron-electron resonance (os-DEER). The long-lived oscillations in the os-DEER spectra were well modeled by a single orientation of the CYP199A2-HaPux complex. The structure is different from the two known Class I CYP-Fdx structures: CYP11A1-Adx and CYP101A1-Pdx. At the protein interface, HaPux residues in the [Fe 2 S 2 ] cluster-binding loop and the α3 helix and the C-terminus residue interact with CYP199A2 residues in the proximal loop and the C helix. These residue contacts are consistent with biochemical data on CYP199A2-ferredoxin binding and electron transfer. Electron-tunneling calculations indicate an efficient electron-transfer pathway from the [Fe 2 S 2 ] cluster to the heme. This new structural model of a CYP-Fdx complex provides the basis for tailoring CYP enzymes for which the cognate ferredoxin is not known, to accept electrons from HaPux and display monooxygenase activity.


  • Organizational Affiliation
    • Centre for Applied Electron Spin Resonance, Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K.

Macromolecule Content 

  • Total Structure Weight: 55.66 kDa 
  • Atom Count: 3,908 
  • Modeled Residue Count: 505 
  • Deposited Residue Count: 505 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:
|   3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CYP199A2A [auth A1]399Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)Mutation(s): 0 
Gene Names: cyp199a2
EC: 1.14.99.15
UniProt
Find proteins for Q6N8N2 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009))
Explore Q6N8N2 
Go to UniProtKB:  Q6N8N2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6N8N2
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|   3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
HaPuxB [auth C1]106Rhodopseudomonas palustris (strain HaA2)Mutation(s): 0 
UniProt
Find proteins for Q2IU01 (Rhodopseudomonas palustris (strain HaA2))
Explore Q2IU01 
Go to UniProtKB:  Q2IU01
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2IU01
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM



Download:Ideal Coordinates CCD File
C [auth A1]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
FES

Query on FES



Download:Ideal Coordinates CCD File
F [auth C1]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ANN

Query on ANN



Download:Ideal Coordinates CCD File
D [auth A1]4-METHOXYBENZOIC ACID
C8 H8 O3
ZEYHEAKUIGZSGI-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
E [auth A1]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Integrative Structure Snapshot

  • Multi-Scale: No 
  • Multi-State: No 
  • Ordered-State: No 
  • Deposited Models: 
  • Representative Model: 

Structure Validation

View Full Validation Report

View Summary Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-10
    Type: Initial release