7A8S
de novo designed ba8-barrel sTIM11 with an alpha-helical extension
Summary for 7A8S
Entry DOI | 10.2210/pdb7a8s/pdb |
Related | 5BVL 6YQY |
Descriptor | sTIM11_h3, 1,2-ETHANEDIOL, CHLORIDE ION, ... (4 entities in total) |
Functional Keywords | protein design, tim-barrel, stim11, de novo protein |
Biological source | synthetic construct |
Total number of polymer chains | 1 |
Total formula weight | 23685.77 |
Authors | Shanmugaratnam, S.,Wiese, J.G.,Hocker, B. (deposition date: 2020-08-31, release date: 2021-03-24, Last modification date: 2024-01-31) |
Primary citation | Wiese, J.G.,Shanmugaratnam, S.,Hocker, B. Extension of a de novo TIM barrel with a rationally designed secondary structure element. Protein Sci., 30:982-989, 2021 Cited by PubMed Abstract: The ability to construct novel enzymes is a major aim in de novo protein design. A popular enzyme fold for design attempts is the TIM barrel. This fold is a common topology for enzymes and can harbor many diverse reactions. The recent de novo design of a four-fold symmetric TIM barrel provides a well understood minimal scaffold for potential enzyme designs. Here we explore opportunities to extend and diversify this scaffold by adding a short de novo helix on top of the barrel. Due to the size of the protein, we developed a design pipeline based on computational ab initio folding that solves a less complex sub-problem focused around the helix and its vicinity and adapt it to the entire protein. We provide biochemical characterization and a high-resolution X-ray structure for one variant and compare it to our design model. The successful extension of this robust TIM-barrel scaffold opens opportunities to diversify it towards more pocket like arrangements and as such can be considered a building block for future design of binding or catalytic sites. PubMed: 33723882DOI: 10.1002/pro.4064 PDB entries with the same primary citation |
Experimental method | X-RAY DIFFRACTION (1.58 Å) |
Structure validation
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