5YL3

Crystal structure of horse heart myoglobin reconstituted with manganese porphycene in resting state at pH 8.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Manganese(V) Porphycene Complex Responsible for Inert C-H Bond Hydroxylation in a Myoglobin Matrix.

Oohora, K.Meichin, H.Kihira, Y.Sugimoto, H.Shiro, Y.Hayashi, T.

(2017) J. Am. Chem. Soc. 139: 18460-18463

  • DOI: 10.1021/jacs.7b11288

  • PubMed Abstract: 
  • A mechanistic study of H2O2-dependent C-H bond hydroxylation by myoglobin reconstituted with a manganese porphycene was carried out. The X-ray crystal structure of the reconstituted protein obtained at 1.5 Å resolution reveals tight incorporation of ...

    A mechanistic study of H2O2-dependent C-H bond hydroxylation by myoglobin reconstituted with a manganese porphycene was carried out. The X-ray crystal structure of the reconstituted protein obtained at 1.5 Å resolution reveals tight incorporation of the complex into the myoglobin matrix at pH 8.5, the optimized pH value for the highest turnover number of hydroxylation of ethylbenzene. The protein generates a spectroscopically detectable two-electron oxidative intermediate in a reaction with peracid, which has a half-life up to 38 s at 10 °C. Electron paramagnetic resonance spectra of the intermediate with perpendicular and parallel modes are silent, indicating formation of a low-spin MnV-oxo species. In addition, the MnV-oxo species is capable of promoting the hydroxylation of sodium 4-ethylbenzenesulfonate under single turnover conditions with an apparent second-order rate constant of 2.0 M-1 s-1 at 25 °C. Furthermore, the higher bond dissociation enthalpy of the substrate decreases the rate constant, in support of the proposal that the H-abstraction is one of the rate-limiting steps. The present engineered myoglobin serves as an artificial metalloenzyme for inert C-H bond activation via a high-valent metal species similar to the species employed by native monooxygenases such as cytochrome P450.


    Related Citations: 
    • C(sp3)-H bond hydroxylation catalyzed by myoglobin reconstituted with manganese porphycene.
      Oohora, K.,Kihira, Y.,Mizohata, E.,Inoue, T.,Hayashi, T.
      (2013) J. Am. Chem. Soc. 135: 17282


    Organizational Affiliation

    Department of Applied Chemistry, Graduate School of Engineering, Osaka University , Suita 565-0871, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Myoglobin
A
154Equus caballusMutation(s): 0 
Gene Names: MB
Find proteins for P68082 (Equus caballus)
Go to Gene View: MB
Go to UniProtKB:  P68082
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
HNN
Query on HNN

Download SDF File 
Download CCD File 
A
PORPHYCENE CONTAINING MN
C34 H36 Mn N4 O4
YIZMGGNKFAWJJG-BWTHIWHLSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 34.575α = 90.00
b = 28.706β = 106.15
c = 62.702γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
Cootmodel building
REFMACphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapanJP15H05804
Japan Society for the Promotion of ScienceJapanJP15H00873
Japan Society for the Promotion of ScienceJapanJP16K14036
Japan Society for the Promotion of ScienceJapanJP16H06045
Japan Society for the Promotion of ScienceJapanJP16H00837
Japan Science and TechnologyJapanJPMJPR15S2

Revision History 

  • Version 1.0: 2017-12-27
    Type: Initial release
  • Version 1.1: 2018-01-17
    Type: Database references