6M8F

Engineered sperm whale myoglobin-based carbene transferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.126 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Origin of high stereocontrol in olefin cyclopropanation catalyzed by an engineered carbene transferase.

Tinoco, A.Wei, Y.Bacik, J.P.Carminati, D.M.Moore, E.J.Ando, N.Zhang, Y.Fasan, R.

(2019) Acs Catalysis 9: 1514-1524

  • DOI: 10.1021/acscatal.8b04073

  • PubMed Abstract: 
  • Recent advances in metalloprotein engineering have led to the development of a myoglobin-based catalyst, Mb(H64V,V68A), capable of promoting the cyclopropanation of vinylarenes with high efficiency and high diastereo- and enantioselectivity. Whereas ...

    Recent advances in metalloprotein engineering have led to the development of a myoglobin-based catalyst, Mb(H64V,V68A), capable of promoting the cyclopropanation of vinylarenes with high efficiency and high diastereo- and enantioselectivity. Whereas many enzymes evolved in nature often exhibit catalytic proficiency and exquisite stereoselectivity, how these features are achieved for a non-natural reaction has remained unclear. In this work, the structural determinants responsible for chiral induction and high stereocontrol in Mb(H64V,V68A)-catalyzed cyclopropanation were investigated via a combination of crystallographic, computational (DFT), and structure-activity analyses. Our results show the importance of steric complementarity and non-covalent interactions involving first-sphere active site residues, heme-carbene, and the olefin substrate, in dictating the stereochemical outcome of the cyclopropanation reaction. High stereocontrol is achieved through two major mechanisms. First, by enforcing a specific conformation of the heme-bound carbene within the active site. Second, by controlling the geometry of attack of the olefin on the carbene via steric occlusion, attractive van der Waals forces and protein-mediated π-π interactions with the olefin substrate. These insights could be leveraged to expand the substrate scope of the myoglobin-based cyclopropanation catalyst toward non-activated olefins and to increase its cyclopropanation activity in the presence of a bulky α-diazo-ester. This work sheds first light into the origin of enzyme-catalyzed enantioselective cyclopropanation, furnishing a mechanistic framework for both understanding the reactivity of current systems and guiding the future development of biological catalysts for this class of synthetically important, abiotic transformations.


    Organizational Affiliation

    Department of Chemistry, University of Rochester, Rochester, NY 14627, United States.,Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, NJ 07030, United States.,Department of Chemistry, Princeton University, Princeton, NJ 08544, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Myoglobin
A
154Physeter macrocephalusMutation(s): 0 
Gene Names: MB
Find proteins for P02185 (Physeter macrocephalus)
Go to Gene View: MB
Go to UniProtKB:  P02185
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SUC
Query on SUC

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Download CCD File 
A
SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
 Ligand Interaction
SO4
Query on SO4

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

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Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.126 
  • Space Group: P 6
Unit Cell:
Length (Å)Angle (°)
a = 90.780α = 90.00
b = 90.780β = 90.00
c = 45.580γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHENIXphasing
SCALAdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-06-12
    Type: Data collection, Database references