8ESU

Myoglobin variant Mb-imi complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.129 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Mechanistic manifold in a hemoprotein-catalyzed cyclopropanation reaction with diazoketone.

Nam, D.Bacik, J.P.Khade, R.L.Aguilera, M.C.Wei, Y.Villada, J.D.Neidig, M.L.Zhang, Y.Ando, N.Fasan, R.

(2023) Nat Commun 14: 7985-7985

  • DOI: https://doi.org/10.1038/s41467-023-43559-7
  • Primary Citation of Related Structures:  
    8ESS, 8ESU

  • PubMed Abstract: 

    Hemoproteins have recently emerged as promising biocatalysts for new-to-nature carbene transfer reactions. However, mechanistic understanding of the interplay between productive and unproductive pathways in these processes is limited. Using spectroscopic, structural, and computational methods, we investigate the mechanism of a myoglobin-catalyzed cyclopropanation reaction with diazoketones. These studies shed light on the nature and kinetics of key catalytic steps in this reaction, including the formation of an early heme-bound diazo complex intermediate, the rate-determining nature of carbene formation, and the cyclopropanation mechanism. Our analyses further reveal the existence of a complex mechanistic manifold for this reaction that includes a competing pathway resulting in the formation of an N-bound carbene adduct of the heme cofactor, which was isolated and characterized by X-ray crystallography, UV-Vis, and Mössbauer spectroscopy. This species can regenerate the active biocatalyst, constituting a non-productive, yet non-destructive detour from the main catalytic cycle. These findings offer a valuable framework for both mechanistic analysis and design of hemoprotein-catalyzed carbene transfer reactions.


  • Organizational Affiliation

    Department of Chemistry, University of Rochester, Rochester, NY, 14627, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Myoglobin154Physeter catodonMutation(s): 2 
Gene Names: MB
EC: 1.11.1 (UniProt), 1.7 (UniProt)
UniProt
Find proteins for P02185 (Physeter macrocephalus)
Explore P02185 
Go to UniProtKB:  P02185
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02185
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.129 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.425α = 90
b = 90.425β = 90
c = 45.442γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-06
    Type: Initial release
  • Version 1.1: 2023-12-13
    Changes: Database references