6QMU
A tetrahedral boronic acid diester formed by a non-natural amino acid in the ligand pocket of an engineered lipocalin
Summary for 6QMU
| Entry DOI | 10.2210/pdb6qmu/pdb |
| Related | 5MHH |
| Descriptor | Neutrophil gelatinase-associated lipocalin, 3-nitrophenol (3 entities in total) |
| Functional Keywords | beta-barrel, p-boronophenylalanine, lipocalin, strep-tag, sugar, transport protein |
| Biological source | Homo sapiens (Human) |
| Total number of polymer chains | 2 |
| Total formula weight | 44019.31 |
| Authors | Skerra, A.,Eichinger, A. (deposition date: 2019-02-08, release date: 2019-08-28, Last modification date: 2024-01-24) |
| Primary citation | Sommer, C.A.,Eichinger, A.,Skerra, A. A Tetrahedral Boronic Acid Diester Formed by an Unnatural Amino Acid in the Ligand Pocket of an Engineered Lipocalin. Chembiochem, 21:469-472, 2020 Cited by PubMed Abstract: Boronic acids have long been known to form cyclic diesters with cis-diol compounds, including many carbohydrates. This phenomenon was previously exploited to create an artificial lectin by incorporating p-borono-l-phenylalanine (Bpa) into the ligand pocket of an engineered lipocalin, resulting in a so-called Borocalin. Here we describe the X-ray analysis of its covalent complex with 4-nitrocatechol as a high-affinity model ligand. As expected, the crystal structure reveals the formation of a cyclic diester between the biosynthetic boronate side chain and the two ortho-hydroxy substituents of the benzene ring. Interestingly, the boron also has a hydroxide ion associated, despite an only moderately basic pH 8.5 in the crystallization buffer. The complex is stabilized by a polar contact to the side chain of Asn134 within the ligand pocket, thus validating the functional design of the Borocalin as an artificial sugar-binding protein. Our structural analysis demonstrates how a boronate can form a thermodynamically stable diester with a vicinal diol in a tetrahedral configuration in aqueous solution near physiological pH. Moreover, our data provide a basis for the further engineering of the Borocalin with the goal of specific recognition of biologically relevant glycans. PubMed: 31390134DOI: 10.1002/cbic.201900405 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.98 Å) |
Structure validation
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