6ZYT
Monomeric streptavidin with a conjugated biotinylated pyrrolidine
This is a non-PDB format compatible entry.
Summary for 6ZYT
| Entry DOI | 10.2210/pdb6zyt/pdb |
| Descriptor | Streptavidin/Rhizavidin Hybrid, SULFATE ION, 5-((3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)-N-((S)-pyrrolidin-3-yl)pentanamide, ... (4 entities in total) |
| Functional Keywords | biotin-binding protein, streptavidin, artificial enzyme, beta-barrel, de novo protein |
| Biological source | Streptomyces avidinii |
| Total number of polymer chains | 6 |
| Total formula weight | 97453.02 |
| Authors | Nodling, A.R.,Lipka-Lloyd, M.,Tsai, Y.H.,Rizkallah, P.,Luk, L.Y.P.,Jin, Y. (deposition date: 2020-08-03, release date: 2021-08-18, Last modification date: 2024-11-06) |
| Primary citation | Nodling, A.R.,Santi, N.,Castillo, R.,Lipka-Lloyd, M.,Jin, Y.,Morrill, L.C.,Swiderek, K.,Moliner, V.,Luk, L.Y.P. The role of streptavidin and its variants in catalysis by biotinylated secondary amines. Org.Biomol.Chem., 19:10424-10431, 2021 Cited by PubMed Abstract: Here, we combine the use of host screening, protein crystallography and QM/MM molecular dynamics simulations to investigate how the protein structure affects iminium catalysis by biotinylated secondary amines in a model 1,4 conjugate addition reaction. Monomeric streptavidin (M-Sav) lacks a quaternary structure and the solvent-exposed reaction site resulted in poor product conversion in the model reaction with low enantio- and regioselectivities. These parameters were much improved when the tetrameric host T-Sav was used; indeed, residues at the symmetrical subunit interface were proven to be critical for catalysis through a mutagenesis study. The use of QM/MM simulations and the asymmetric dimeric variant D-Sav revealed that both Lys121 residues which are located in the hosting and neighboring subunits play a critical role in controlling the stereoselectivity and reactivity. Lastly, the D-Sav template, though providing a lower conversion than that of the symmetric tetrameric counterpart, is likely a better starting point for future protein engineering because each surrounding residue within the asymmetric scaffold can be refined for secondary amine catalysis. PubMed: 34825690DOI: 10.1039/d1ob01947c PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.8 Å) |
Structure validation
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