6I37

Crystal structure of nv1Pizza6-AYW, a circularly permuted designer protein

• PDB DOI:  https://doi.org/10.2210/pdb6I37/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2018-11-05 Released: 2019-11-20 
• Deposition Author(s): Mylemans, B., Noguchi, H., Deridder, E., Voet, A.R.D.
• Funding Organization(s): Research Foundation - Flanders

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.224 
• R-Value Work: 0.190 
• R-Value Observed: 0.191 

Literature

Influence of circular permutations on the structure and stability of a six-fold circular symmetric designer protein.

Mylemans, B., Noguchi, H., Deridder, E., Lescrinier, E., Tame, J.R.H., Voet, A.R.D.

(2020) Protein Sci 

• PubMed: 33006397 
• DOI: https://doi.org/10.1002/pro.3961
• Primary Citation of Related Structures:  
  6I37, 6I38, 6I39, 6I3A, 6I3B


• PubMed Abstract: 
  

The β-propeller fold is adopted by a sequentially diverse family of repeat proteins with apparent rotational symmetry. While the structure is mostly stabilized by hydrophobic interactions, an additional stabilization is provided by hydrogen bonds between the N-and C-termini, which are almost invariably part of the same β-sheet. This feature is often referred to as the "Velcro" closure. The positioning of the termini within a blade is variable and depends on the protein family. In order to investigate the influence of this location on protein structure, folding and stability, we created different circular permutants, and a circularized version, of the designer propeller protein named Pizza. This protein is perfectly symmetrical, possessing six identical repeats. While all mutants adopt the same structure, the proteins lacking the "Velcro" closure were found to be significantly less resistant to thermal and chemical denaturation. This could explain why such proteins are rarely observed in nature. Interestingly the most common "Velcro" configuration for this protein family was not the most stable among the Pizza variants tested. The circularized version shows dramatically improved stability, which could have implications for future applications.

---

Organizational Affiliation: 

Department of Chemistry, KU Leuven, Leuven, Belgium.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 26.14 kDa 
• Atom Count: 2,261 
• Modelled Residue Count: 251 
• Deposited Residue Count: 255 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
nv1Pizza6-AYW	A	255	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.224 
• R-Value Work: 0.190 
• R-Value Observed: 0.191 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.256	α = 90
b = 55.977	β = 90
c = 69.352	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-11-20 
Deposition Author(s): Mylemans, B., Noguchi, H., Deridder, E., Voet, A.R.D.

---

Funding Organization	Location	Grant Number
Research Foundation - Flanders	Belgium	G0F9316N
Research Foundation - Flanders	Belgium	G051917N
Research Foundation - Flanders	Belgium	GBM-D3229-ASP/17

Revision History  

• Version 1.0: 2019-11-20
  Type: Initial release
  
• Version 1.1: 2020-10-21
  Changes: Database references