6VXE
Crystal structure of hydroxyproline dehydratase (HypD) from Clostridioides difficile with substrate trans-4-hydroxy-L-proline bound
Summary for 6VXE
| Entry DOI | 10.2210/pdb6vxe/pdb |
| Descriptor | Trans-4-hydroxy-L-proline dehydratase, 4-HYDROXYPROLINE (3 entities in total) |
| Functional Keywords | glycyl radical enzyme, hydroxyproline dehydratase, lyase |
| Biological source | Clostridioides difficile 70-100-2010 |
| Total number of polymer chains | 8 |
| Total formula weight | 732701.91 |
| Authors | Backman, L.R.F.,Drennan, C.L. (deposition date: 2020-02-21, release date: 2020-04-08, Last modification date: 2023-10-11) |
| Primary citation | Backman, L.R.,Huang, Y.Y.,Andorfer, M.C.,Gold, B.,Raines, R.T.,Balskus, E.P.,Drennan, C.L. Molecular basis for catabolism of the abundant metabolitetrans-4-hydroxy-L-proline by a microbial glycyl radical enzyme. Elife, 9:-, 2020 Cited by PubMed Abstract: The glycyl radical enzyme (GRE) superfamily utilizes a glycyl radical cofactor to catalyze difficult chemical reactions in a variety of anaerobic microbial metabolic pathways. Recently, a GRE, -4-hydroxy-L-proline (Hyp) dehydratase (HypD), was discovered that catalyzes the dehydration of Hyp to ()-Δ-pyrroline-5-carboxylic acid (P5C). This enzyme is abundant in the human gut microbiome and also present in prominent bacterial pathogens. However, we lack an understanding of how HypD performs its unusual chemistry. Here, we have solved the crystal structure of HypD from the pathogen with Hyp bound in the active site. Biochemical studies have led to the identification of key catalytic residues and have provided insight into the radical mechanism of Hyp dehydration. PubMed: 32180548DOI: 10.7554/eLife.51420 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.464 Å) |
Structure validation
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