8T7J

Oxygen- and PLP-dependent Cap15 holoenzyme bound with phosphate anion

8T7J の概要

• エントリーDOI: 10.2210/pdb8t7j/pdb
• 分子名称: Putative selenocysteine synthase, 1,2-ETHANEDIOL, PHOSPHATE ION, ... (4 entities in total)
• 機能のキーワード: pyridoxal 5'-phosphate, monooxygenase-decarboxylase, type i fold, biosynthetic protein
• 由来する生物種: Streptomyces sp. SANK 62799
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 169639.28

構造登録者

Daniel-Ivad, P.,Ryan, K.S. (登録日: 2023-06-20, 公開日: 2023-08-23, 最終更新日: 2023-11-15)

主引用文献

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

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: 37556254
DOI: 10.1021/acs.biochem.3c00216

実験手法

X-RAY DIFFRACTION (2.4 Å)