6FH8

E. coli surface display of streptavidin for directed evolution of an allylic deallocase

• PDB DOI: https://doi.org/10.2210/pdb6FH8/pdb

• Classification: biotin binding protein
• Organism(s): Streptomyces avidinii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-01-12 Released: 2018-08-22 
• Deposition Author(s): Heinisch, T., Schwizer, F., Garabedian, B., Csibra, E., Jeschek, M., Pinheiro Bernhardes, V., Marliere, P., Panke, S., Ward, T.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.159 
• R-Value Work: 0.120 
• R-Value Observed: 0.122 

Literature

E. colisurface display of streptavidin for directed evolution of an allylic deallylase.

Heinisch, T., Schwizer, F., Garabedian, B., Csibra, E., Jeschek, M., Vallapurackal, J., Pinheiro, V.B., Marliere, P., Panke, S., Ward, T.R.

(2018) Chem Sci 9: 5383-5388

• PubMed: 30079176 
• DOI: https://doi.org/10.1039/c8sc00484f
• Primary Citation of Related Structures:  
  6FH8


• PubMed Abstract: 
  

  Artificial metalloenzymes (ArMs hereafter) combine attractive features of both homogeneous catalysts and enzymes and offer the potential to implement new-to-nature reactions in living organisms. Herein we present an E. coli surface display platform for streptavidin (Sav hereafter) relying on an Lpp-OmpA anchor. The system was used for the high throughput screening of a bioorthogonal CpRu-based artificial deallylase (ADAse) that uncages an allylcarbamate-protected aminocoumarin 1 . Two rounds of directed evolution afforded the double mutant S112M-K121A that displayed a 36-fold increase in surface activity vs. cellular background and a 5.7-fold increased in vitro activity compared to the wild type enzyme. The crystal structure of the best ADAse reveals the importance of mutation S112M to stabilize the cofactor conformation inside the protein.

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Organizational Affiliation: 

Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel CH-4002 , Switzerland . Email: [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 17.22 kDa 
• Atom Count: 1,065 
• Modelled Residue Count: 125 
• Deposited Residue Count: 159 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A	159	Streptomyces avidinii	Mutation(s): 2
UniProt
Find proteins for P22629 (Streptomyces avidinii) Explore P22629  Go to UniProtKB:  P22629

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JCT	B [auth A]	biotinylated ruthenium cyclopentadienide C29 H28 N5 O5 Ru S CQAGRAKHOFYKGA-XRCFJZOASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.159 
• R-Value Work: 0.120 
• R-Value Observed: 0.122 
• Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.722	α = 90
b = 57.722	β = 90
c = 183.615	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-22 
Deposition Author(s): Heinisch, T., Schwizer, F., Garabedian, B., Csibra, E., Jeschek, M., Pinheiro Bernhardes, V., Marliere, P., Panke, S., Ward, T.R.

Revision History  

• Version 1.0: 2018-08-22
  Type: Initial release