6REK

Crystal structure of Pizza6-SH with Cu2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.142 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Artificial beta-propeller protein-based hydrolases.

Clarke, D.E.Noguchi, H.Gryspeerdt, J.A.G.De Feyter, S.Voet, A.R.D.

(2019) Chem Commun (Camb) 55: 8880-8883

  • DOI: 10.1039/c9cc04388h
  • Primary Citation of Related Structures:  
    6REG, 6REH, 6REJ, 6REK, 6REN

  • PubMed Abstract: 
  • We developed an artificial hydrolase based on the symmetrical Pizza6 β-propeller protein for the metal-free hydrolysis of 4-nitrophenyl acetate and butyrate. Through site-specific mutagenesis and crystallisation studies, the catalytic mechanism was investigated and found to be dependent on a threonine-histidine dyad ...

    We developed an artificial hydrolase based on the symmetrical Pizza6 β-propeller protein for the metal-free hydrolysis of 4-nitrophenyl acetate and butyrate. Through site-specific mutagenesis and crystallisation studies, the catalytic mechanism was investigated and found to be dependent on a threonine-histidine dyad. The mutant with additional histidine residues generated the highest kcat values, forming a His-His-Thr triad and matched previously reported metalloenzymes. The highly symmetrical β-propeller artificial enzymes and their protein-metal complexes have potential to be utilised in bioinorganic and supramolecular chemistry, as well as being developed further into 2D/3D catalytic materials.


    Organizational Affiliation

    Division of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001, Leuven, Belgium.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pizza6-SHA256synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CU (Subject of Investigation/LOI)
Query on CU

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.142 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.708α = 90
b = 69.547β = 109.16
c = 48.266γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Foundation - FlandersBelgiumG0E4717N, G0F9316N, G051917N

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-31
    Type: Initial release