6T32 | pdb_00006t32

Streptavidin variants harbouring an artificial organocatalyst based cofactor

• PDB DOI: https://doi.org/10.2210/pdb6T32/pdb

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


• Deposited: 2019-10-10 Released: 2020-11-18 
• Deposition Author(s): Lechner, H., Hocker, B.
• Funding Organization(s): Austrian Science Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.191 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

An Artificial Cofactor Catalyzing the Baylis-Hillman Reaction with Designed Streptavidin as Protein Host*.

Lechner, H., Emann, V.R., Breuning, M., Hocker, B.

(2021) Chembiochem 22: 1573-1577

• PubMed: 33400831 
• DOI: https://doi.org/10.1002/cbic.202000880
• Primary Citation Related Structures: 
  6T1E, 6T1G, 6T1K, 6T2L, 6T2Y, 6T2Z, 6T30, 6T31, 6T32


• PubMed Abstract: 
  

  An artificial cofactor based on an organocatalyst embedded in a protein has been used to conduct the Baylis-Hillman reaction in a buffered system. As protein host, we chose streptavidin, as it can be easily crystallized and thereby supports the design process. The protein host around the cofactor was rationally designed on the basis of high-resolution crystal structures obtained after each variation of the amino acid sequence. Additionally, DFT-calculated intermediates and transition states were used to rationalize the observed activity. Finally, repeated cycles of structure determination and redesign led to a system with an up to one order of magnitude increase in activity over the bare cofactor and to the most active proteinogenic catalyst for the Baylis-Hillman reaction known today.

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Organizational Affiliation: 
• Department of Biochemistry, University Bayreuth, Universitätsstrasse 30, 95447, Bayreuth, Germany.
Organic Chemistry, University Bayreuth, Universitätsstrasse 30, 95447, Bayreuth, Germany.

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: gel filtration

Macromolecule Content 

• Total Structure Weight: 33.87 kDa 
• Atom Count: 2,105 
• Modeled Residue Count: 242 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A, B	159	Streptomyces avidinii	Mutation(s): 7
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
HL9 (Subject of Investigation/LOI)	C [auth A], D [auth B]	5-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-(1-pyridin-4-ylpiperidin-4-yl)pentanamide C20 H29 N5 O2 S GEHXEZPHNHPYOB-LNLFQRSKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.191 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.33	α = 90
b = 85.085	β = 90
c = 99.444	γ = 90

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-11-18 
Deposition Author(s): Lechner, H., Hocker, B.

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Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	J 3994

Revision History  

• Version 1.0: 2020-11-18
  Type: Initial release
  
• Version 1.1: 2021-05-05
  Changes: Database references
• Version 1.2: 2021-05-12
  Changes: Database references
• Version 1.3: 2024-01-24
  Changes: Advisory, Data collection, Database references, Refinement description