7B74

Chimeric Streptavidin With A Dimerization Domain For Artificial Transfer Hydrogenation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.191 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Spiers Memorial Lecture: Shielding the active site: a streptavidin superoxide-dismutase chimera as a host protein for asymmetric transfer hydrogenation.

Igareta, N.V.Tachibana, R.Spiess, D.C.Peterson, R.L.Ward, T.R.

(2023) Faraday Discuss 

  • DOI: https://doi.org/10.1039/d3fd00034f
  • Primary Citation of Related Structures:  
    7B74

  • PubMed Abstract: 

    By anchoring a metal cofactor within a host protein, so-called artificial metalloenzymes can be generated. Such hybrid catalysts combine the versatility of transition metals in catalyzing new-to-nature reactions with the power of genetic-engineering to evolve proteins. With the aim of gaining better control over second coordination-sphere interactions between a streptavidin host-protein (Sav) and a biotinylated cofactor, we engineered a hydrophobic dimerization domain, borrowed from superoxide dismutase C (SOD), on Sav's biotin-binding vestibule. The influence of the SOD dimerization domain (DD) on the performance of an asymmetric transfer hydrogenase (ATHase) resulting from anchoring a biotinylated Cp*Ir-cofactor - [Cp*Ir(biot- p -L)Cl] (1-Cl) - within Sav-SOD is reported herein. We show that, depending on the nature of the residue at position Sav S112, the introduction of the SOD DD on the biotin-binding vestibule leads to an inversion of configuration of the reduction product, as well as a fivefold increase in catalytic efficiency. The findings are rationalized by QM/MM calculations, combined with X-ray crystallography.


  • Organizational Affiliation

    Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, Basel, CH-4058, Switzerland. thomas.ward@unibas.ch.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Streptavidin,Superoxide dismutase [Cu-Zn],StreptavidinA [auth AAA],
B [auth BBB],
C [auth CCC],
D [auth DDD]
194Streptomyces avidiniiMycobacterium tuberculosis variant bovis AF2122/97Mutation(s): 1 
EC: 1.15.1.1
UniProt
Find proteins for P22629 (Streptomyces avidinii)
Explore P22629 
Go to UniProtKB:  P22629
Find proteins for P0A609 (Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97))
Explore P0A609 
Go to UniProtKB:  P0A609
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP22629P0A609
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4IR (Subject of Investigation/LOI)
Query on 4IR

Download Ideal Coordinates CCD File 
E [auth AAA],
F [auth BBB],
G [auth CCC],
H [auth DDD]
{N-(4-{[2-(amino-kappaN)ethyl]sulfamoyl-kappaN}phenyl)-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide}(chloro)[(1,2,3,4,5-eta)-1,2,3,4,5-pentamethylcyclopentadienyl]iridium(III)
C28 H45 Cl Ir N5 O4 S2
OPJZDGOSRZOXTM-DYKJULMGSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.285α = 90
b = 57.307β = 94.616
c = 88.035γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-17
    Type: Initial release
  • Version 1.1: 2023-06-07
    Changes: Database references, Derived calculations
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description