8QBC

Reactive amide intermediate in sperm whale myoglobin mutant H64V V68A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Myoglobin-Catalyzed Azide Reduction Proceeds via an Anionic Metal Amide Intermediate.

Tinzl, M.Diedrich, J.V.Mittl, P.R.E.Clemancey, M.Reiher, M.Proppe, J.Latour, J.M.Hilvert, D.

(2024) J Am Chem Soc 146: 1957-1966

  • DOI: https://doi.org/10.1021/jacs.3c09279
  • Primary Citation of Related Structures:  
    8QBA, 8QBC

  • PubMed Abstract: 

    Nitrene transfer reactions catalyzed by heme proteins have broad potential for the stereoselective formation of carbon-nitrogen bonds. However, competition between productive nitrene transfer and the undesirable reduction of nitrene precursors limits the broad implementation of such biocatalytic methods. Here, we investigated the reduction of azides by the model heme protein myoglobin to gain mechanistic insights into the factors that control the fate of key reaction intermediates. In this system, the reaction proceeds via a proposed nitrene intermediate that is rapidly reduced and protonated to give a reactive ferrous amide species, which we characterized by UV/vis and Mössbauer spectroscopies, quantum mechanical calculations, and X-ray crystallography. Rate-limiting protonation of the ferrous amide to produce the corresponding amine is the final step in the catalytic cycle. These findings contribute to our understanding of the heme protein-catalyzed reduction of azides and provide a guide for future enzyme engineering campaigns to create more efficient nitrene transferases. Moreover, harnessing the reduction reaction in a chemoenzymatic cascade provided a potentially practical route to substituted pyrroles.


  • Organizational Affiliation

    Laboratory of Organic Chemistry, ETH Zürich, 8093 Zürich, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Myoglobin155Physeter macrocephalusMutation(s): 0 
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

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.842α = 90
b = 47.157β = 90
c = 76.241γ = 90
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
Other governmentSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-13
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Database references