7UTE

MicroED structure of Aeropyrum pernix protoglobin mutant


Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 2.10 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Biocatalytic Carbene Transfer Using Diazirines.

Porter, N.J.Danelius, E.Gonen, T.Arnold, F.H.

(2022) J Am Chem Soc 144: 8892-8896

  • DOI: https://doi.org/10.1021/jacs.2c02723
  • Primary Citation of Related Structures:  
    7UTE

  • PubMed Abstract: 

    Biocatalytic carbene transfer from diazo compounds is a versatile strategy in asymmetric synthesis. However, the limited pool of stable diazo compounds constrains the variety of accessible products. To overcome this restriction, we have engineered variants of Aeropyrum pernix protoglobin ( Ape Pgb) that use diazirines as carbene precursors. While the enhanced stability of diazirines relative to their diazo isomers enables access to a diverse array of carbenes, they have previously resisted catalytic activation. Our engineered Ape Pgb variants represent the first example of catalysts for selective carbene transfer from these species at room temperature. The structure of an Ape Pgb variant, determined by microcrystal electron diffraction (MicroED), reveals that evolution has enhanced access to the heme active site to facilitate this new-to-nature catalysis. Using readily prepared aryl diazirines as model substrates, we demonstrate the application of these highly stable carbene precursors in biocatalytic cyclopropanation, N-H insertion, and Si-H insertion reactions.


  • Organizational Affiliation

    Division of Chemistry and Chemical Engineering, Division of Biology and Bioengineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, California 91125, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protogloblin ApPgb
A, B, C, D
195Aeropyrum pernixMutation(s): 0 
Gene Names: APE_0287
UniProt
Find proteins for Q9YFF4 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1))
Explore Q9YFF4 
Go to UniProtKB:  Q9YFF4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9YFF4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 2.10 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.246α = 104.08
b = 58.305β = 98.59
c = 80.732γ = 90.1
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONPHENIX1.20.1-4487-000

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM136508
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-25
    Type: Initial release
  • Version 1.1: 2022-06-08
    Changes: Database references
  • Version 1.2: 2024-02-14
    Changes: Data collection
  • Version 1.3: 2024-04-03
    Changes: Refinement description