7OEX
Crystal structure of RBBP9 in complex with phenylalanine
Summary for 7OEX
| Entry DOI | 10.2210/pdb7oex/pdb |
| Related | 2QS9 |
| Descriptor | Serine hydrolase RBBP9, PHENYLALANINE (3 entities in total) |
| Functional Keywords | hydrolase, retinoblastoma-binding protein 9 |
| Biological source | Homo sapiens (Human) |
| Total number of polymer chains | 2 |
| Total formula weight | 44524.49 |
| Authors | Fiedler, M.,Tang, S.,Chin, J.W. (deposition date: 2021-05-04, release date: 2021-12-22, Last modification date: 2024-01-31) |
| Primary citation | Tang, S.,Beattie, A.T.,Kafkova, L.,Petris, G.,Huguenin-Dezot, N.,Fiedler, M.,Freeman, M.,Chin, J.W. Mechanism-based traps enable protease and hydrolase substrate discovery. Nature, 602:701-707, 2022 Cited by PubMed Abstract: Hydrolase enzymes, including proteases, are encoded by 2-3% of the genes in the human genome and 14% of these enzymes are active drug targets. However, the activities and substrate specificities of many proteases-especially those embedded in membranes-and other hydrolases remain unknown. Here we report a strategy for creating mechanism-based, light-activated protease and hydrolase substrate traps in complex mixtures and live mammalian cells. The traps capture substrates of hydrolases, which normally use a serine or cysteine nucleophile. Replacing the catalytic nucleophile with genetically encoded 2,3-diaminopropionic acid allows the first step reaction to form an acyl-enzyme intermediate in which a substrate fragment is covalently linked to the enzyme through a stable amide bond; this enables stringent purification and identification of substrates. We identify new substrates for proteases, including an intramembrane mammalian rhomboid protease RHBDL4 (refs. ). We demonstrate that RHBDL4 can shed luminal fragments of endoplasmic reticulum-resident type I transmembrane proteins to the extracellular space, as well as promoting non-canonical secretion of endogenous soluble endoplasmic reticulum-resident chaperones. We also discover that the putative serine hydrolase retinoblastoma binding protein 9 (ref. ) is an aminopeptidase with a preference for removing aromatic amino acids in human cells. Our results exemplify a powerful paradigm for identifying the substrates and activities of hydrolase enzymes. PubMed: 35173328DOI: 10.1038/s41586-022-04414-9 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.51 Å) |
Structure validation
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