6TJC

Crystal structure of the computationally designed Cake3 protein

Summary for 6TJC

• Entry DOI: 10.2210/pdb6tjc/pdb
• Descriptor: Cake3, PHOSPHATE ION, GLYCEROL, ... (4 entities in total)
• Functional Keywords: beta-propeller, computationally designed, symmetrical, repeat protein, de novo protein
• Biological source: synthetic construct
• Total number of polymer chains: 3
• Total formula weight: 40695.14

Authors

Laier, I.,Mylemans, B.,Voet, A.R.D.,Noguchi, H. (deposition date: 2019-11-26, release date: 2020-05-06, Last modification date: 2024-05-01)

Primary citation

Mylemans, B.,Laier, I.,Kamata, K.,Akashi, S.,Noguchi, H.,Tame, J.R.H.,Voet, A.R.D.
Structural plasticity of a designer protein sheds light on beta-propeller protein evolution.
Febs J., 288:530-545, 2021

PubMed Abstract: β-propeller proteins are common in nature, where they are observed to adopt 4- to 10-fold internal rotational pseudo-symmetry. This size diversity can be explained by the evolutionary process of gene duplication and fusion. In this study, we investigated a distorted β-propeller protein, an apparent intermediate between two symmetries. From this template, we created a perfectly symmetric 9-bladed β-propeller named Cake, using computational design and ancestral sequence reconstruction. The designed repeat sequence was found to be capable of generating both 8-fold and 9-fold propellers which are highly stable. Cake variants with 2-10 identical copies of the repeat sequence were characterised by X-ray crystallography and in solution. They were found to be highly stable, and to self-assemble into 8- or 9-fold symmetrical propellers. These findings show that the β-propeller fold allows sufficient structural plasticity to permit a given blade to assemble different forms, a transition from even to odd changes in blade number, and provide a potential explanation for the wide diversity of repeat numbers observed in natural propeller proteins. DATABASE: Structural data are available in Protein Data Bank database under the accession numbers 6TJB, 6TJC, 6TJD, 6TJE, 6TJF, 6TJG, 6TJH and 6TJI.

PubMed: 32343866
DOI: 10.1111/febs.15347

Experimental method

X-RAY DIFFRACTION (1.9 Å)