8T7J
Oxygen- and PLP-dependent Cap15 holoenzyme bound with phosphate anion
Summary for 8T7J
| Entry DOI | 10.2210/pdb8t7j/pdb |
| Descriptor | Putative selenocysteine synthase, 1,2-ETHANEDIOL, PHOSPHATE ION, ... (4 entities in total) |
| Functional Keywords | pyridoxal 5'-phosphate, monooxygenase-decarboxylase, type i fold, biosynthetic protein |
| Biological source | Streptomyces sp. SANK 62799 |
| Total number of polymer chains | 4 |
| Total formula weight | 169639.28 |
| Authors | Daniel-Ivad, P.,Ryan, K.S. (deposition date: 2023-06-20, release date: 2023-08-23, Last modification date: 2023-11-15) |
| Primary citation | Daniel-Ivad, P.G.,Van Lanen, S.,Ryan, K.S. Structure of the Oxygen, Pyridoxal Phosphate-Dependent Capuramycin Biosynthetic Protein Cap15. Biochemistry, 62:2611-2621, 2023 Cited by PubMed Abstract: Pyridoxal phosphate-dependent enzymes able to use oxygen as a co-substrate have emerged in multiple protein families. Here, we use crystallography to solve the 2.40 Å resolution crystal structure of Cap15, a nucleoside biosynthetic enzyme that catalyzes the oxidative decarboxylation of glycyl uridine. Our structural study captures the internal aldimine, pinpointing the active site lysine as K230 and showing the site of phosphate binding. Our docking studies reveal how Cap15 is able to catalyze a stereoselective deprotonation reaction, and bioinformatic analysis reveals active site residues that distinguish Cap15 from the structurally related d-glucosaminate-6-phosphate ammonia lyase and l-seryl-tRNA(Sec) selenium transferase (SelA). Our work provides the structural basis for further mechanistic investigation of a unique biosynthetic enzyme and provides a blueprint for understanding how oxygen reactivity emerged in the SelA-like protein family. PubMed: 37556254DOI: 10.1021/acs.biochem.3c00216 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.4 Å) |
Structure validation
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