6GMI

Genetic Engineering of an Artificial Metalloenzyme for Transfer Hydrogenation of a Self-Immolative Substrate in E. coli's Periplasm.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Genetic Engineering of an Artificial Metalloenzyme for Transfer Hydrogenation of a Self-Immolative Substrate in Escherichia coli's Periplasm.

Zhao, J.Rebelein, J.G.Mallin, H.Trindler, C.Pellizzoni, M.M.Ward, T.R.

(2018) J Am Chem Soc 140: 13171-13175

  • DOI: https://doi.org/10.1021/jacs.8b07189
  • Primary Citation of Related Structures:  
    6GMI

  • PubMed Abstract: 

    Artificial metalloenzymes (ArMs), which combine an abiotic metal cofactor with a protein scaffold, catalyze various synthetically useful transformations. To complement the natural enzymes' repertoire, effective optimization protocols to improve ArM's performance are required. Here we report on our efforts to optimize the activity of an artificial transfer hydrogenase (ATHase) using Escherichia coli whole cells. For this purpose, we rely on a self-immolative quinolinium substrate which, upon reduction, releases fluorescent umbelliferone, thus allowing efficient screening. Introduction of a loop in the immediate proximity of the Ir-cofactor afforded an ArM with up to 5-fold increase in transfer hydrogenation activity compared to the wild-type ATHase using purified mutants.


  • Organizational Affiliation

    Department of Chemistry , University of Basel , Mattenstrasse 24a, BPR 1096 , CH-4058 Basel , Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Streptavidin181Streptomyces avidiniiMutation(s): 2 
UniProt
Find proteins for P22629 (Streptomyces avidinii)
Explore P22629 
Go to UniProtKB:  P22629
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22629
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4IR
Query on 4IR

Download Ideal Coordinates CCD File 
B [auth A]{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
IR3
Query on IR3

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A]
IRIDIUM (III) ION
Ir
MILUBEOXRNEUHS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.507α = 90
b = 57.507β = 90
c = 184.13γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland200020_162348
European Research CouncilDrEAM
Swiss National Science FoundationSwitzerlandNCCR MSE
European Molecular Biology OrganizationGermanyALTF 194-2017

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2018-10-31
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description