8WF5

Horse heart myoglobin reconstituted with an iron complex of porphyrin bearing two CF3 groups (rMb(FePor(CF3)2))


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.157 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Redox Engineering of Myoglobin by Cofactor Substitution to Enhance Cyclopropanation Reactivity.

Kagawa, Y.Oohora, K.Himiyama, T.Suzuki, A.Hayashi, T.

(2024) Angew Chem Int Ed Engl : e202403485-e202403485

  • DOI: https://doi.org/10.1002/anie.202403485
  • Primary Citation of Related Structures:  
    8WF5

  • PubMed Abstract: 

    Design of metal cofactor ligands is essential for controlling the reactivity of metalloenzymes. We investigated a carbene transfer reaction catalyzed by myoglobins containing iron porphyrin cofactors with one and two trifluoromethyl groups at peripheral sites (FePorCF3 and FePor(CF3)2, respectively), native heme and iron porphycene (FePc). These four myoglobins show a wide range of Fe(II)/Fe(III) redox potentials in the protein of +147 mV, +87 mV, +42 mV and -198 mV vs NHE, respectively. Myoglobin reconstituted with FePor(CF3)2 has a more positive potential which enhances the reactivity of a carbene intermediate with alkenes and demonstrates superior cyclopropanation of inert alkenes such as aliphatic and internal alkenes. In contrast, engineered myoglobin reconstituted with FePc has a more negative redox potential, which accelerates the formation of the intermediate but has low reactivity for inert alkenes. Mechanistic studies indicate that myoglobin with FePor(CF3)2 generates an undetectable active intermediate with a radical character. In contrast, this reaction catalyzed by myoglobin with FePc includes a detectable iron-carbene species with electrophilic character. This finding highlights the importance of redox-focused design of the iron porphyrinoid cofactor in hemoproteins to tune the reactivity of the carbene transfer reaction.


  • Organizational Affiliation

    Osaka University, Department of Applied Chemistry, JAPAN.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Myoglobin153Equus caballusMutation(s): 0 
UniProt
Find proteins for P68082 (Equus caballus)
Explore P68082 
Go to UniProtKB:  P68082
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68082
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.157 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.26α = 90
b = 28.74β = 105.472
c = 63.65γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP15H05804
Japan Society for the Promotion of Science (JSPS)JapanJP18KK0156
Japan Society for the Promotion of Science (JSPS)JapanJP20H02755
Japan Society for the Promotion of Science (JSPS)JapanJP20H00403
Japan Society for the Promotion of Science (JSPS)JapanJP20KK0315
Japan Society for the Promotion of Science (JSPS)JapanJP22H05364
Japan Society for the Promotion of Science (JSPS)JapanJP22K21348
Japan Society for the Promotion of Science (JSPS)JapanJP23H03832
Japan Science and TechnologyJapanJPMJPR15S2
Japan Science and TechnologyJapanJPMJPR22A3
Japan Society for the Promotion of Science (JSPS)JapanJP21J20563

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-12
    Type: Initial release