6Z4R

sperm whale myoglobin mutant (H64V V64A) bearing the non-canonical amino acid 3-thienylalanine as axial heme ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Noncanonical Heme Ligands Steer Carbene Transfer Reactivity in an Artificial Metalloenzyme*.

Pott, M.Tinzl, M.Hayashi, T.Ota, Y.Dunkelmann, D.Mittl, P.R.E.Hilvert, D.

(2021) Angew Chem Int Ed Engl 60: 15063-15068

  • DOI: https://doi.org/10.1002/anie.202103437
  • Primary Citation of Related Structures:  
    6Z4R, 6Z4T

  • PubMed Abstract: 

    Changing the primary metal coordination sphere is a powerful strategy for tuning metalloprotein properties. Here we used amber stop codon suppression with engineered pyrrolysyl-tRNA synthetases, including two newly evolved enzymes, to replace the proximal histidine in myoglobin with N δ -methylhistidine, 5-thiazoylalanine, 4-thiazoylalanine and 3-(3-thienyl)alanine. In addition to tuning the heme redox potential over a >200 mV range, these noncanonical ligands modulate the protein's carbene transfer activity with ethyl diazoacetate. Variants with increased reduction potential proved superior for cyclopropanation and N-H insertion, whereas variants with reduced E o values gave higher S-H insertion activity. Given the functional importance of histidine in many enzymes, these genetically encoded analogues could be valuable tools for probing mechanism and enabling new chemistries.


  • 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
Myoglobin154Physeter macrocephalusMutation(s): 3 
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
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.063α = 90
b = 47.26β = 90
c = 76.213γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXmodel building
PHENIXphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-28
    Type: Initial release
  • Version 1.1: 2021-06-30
    Changes: Database references
  • Version 2.0: 2023-09-13
    Changes: Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Structure summary
  • Version 2.1: 2024-01-24
    Changes: Refinement description