6vxe | pdb_00006vxe

Crystal structure of hydroxyproline dehydratase (HypD) from Clostridioides difficile with substrate trans-4-hydroxy-L-proline bound

spinqualitylabelsall models 6vxe, resolution 2.46Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6vxe is a 8 chain structure with sequence from Clostridioides difficile 70-100-2010. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.464Å Ligands: HYP Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function HYPD_CLODI Glycine radical enzyme that catalyzes the dehydration of the non-proteinogenic amino acid trans-4-hydroxy-L-proline (Hyp) to produce delta(1)-pyrroline-5-carboxylate (P5C). Is involved in the anaerobic degradation of 4-hydroxyproline. Publication Abstract from PubMed 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, trans-4-hydroxy-L-proline (Hyp) dehydratase (HypD), was discovered that catalyzes the dehydration of Hyp to (S)-Delta(1)-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 Clostridioides difficile 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. Molecular basis for catabolism of the abundant metabolite trans-4-hydroxy-L-proline by a microbial glycyl radical enzyme.,Backman LR, Huang YY, Andorfer MC, Gold B, Raines RT, Balskus EP, Drennan CL Elife. 2020 Mar 17;9. pii: 51420. doi: 10.7554/eLife.51420. PMID:32180548 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also HypA%2C HypB%2C HypC%2C HypD%2C HypE and HypF 3D structures

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