9LO3

Transition state analogue(GMPK in complex with GMP, ADP, Mg2+ and AlF4- at 277 K)

9LO3 の概要

• エントリーDOI: 10.2210/pdb9lo3/pdb
• 分子名称: Guanylate kinase, MAGNESIUM ION, GUANOSINE-5'-MONOPHOSPHATE, ... (8 entities in total)
• 機能のキーワード: guanylate kinase, transferase
• 由来する生物種: Homo sapiens (human)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 23143.79

構造登録者

Wang, L.,Ruan, K. (登録日: 2025-01-22, 公開日: 2025-09-10)

主引用文献

Wang, L.,Li, Z.,Xuan, Y.,Qin, J.,Li, S.,Zhong, F.,Song, Y.,Yang, K.,Lv, M.,Li, F.,Jiahai, Z.,Pan, Y.,Guang, S.,Zhao, Y.,Shi, Y.,Liu, X.,Du, Y.,Gao, J.,Ruan, K.
Comprehensive profiling of the catalytic conformations of human Guanylate kinase.
Nat Commun, 16:6859-6859, 2025

PubMed Abstract: Human guanylate kinase (GMPK) as the sole enzyme for GDP biosynthesis plays pivotal roles in antiviral prodrug activation and tumorigenesis. Despite its biological significance, the catalytic mechanism remains poorly understood. Here, we resolve crystal structures of GMPK in free and GMP-bound form, revealing the interdomain motions of GMPBD and LID relative to the CORE domain. Biochemical assays demonstrate potassium's dual functionality in substrate recognition and phosphoryl transfer catalysis. Structural analyses uncover intradomain conformational motion within the LID domain and essential interactions for ADP/ATP binding. Notably, the cooperative ATPγS binding potentiated by prior GMP binding are structurally elucidated. Three key complexes, pre-reaction state (GMP/ATPγS), transition state (AlF mimic), and post-reaction state (GDP/ADP), collectively delineate the reversible catalytic pathway. This comprehensive structural characterization of GMPK's dynamic landscape establishes a foundation for developing conformation-specific inhibitors through structure-guided drug design.

PubMed: 40715061
DOI: 10.1038/s41467-025-61732-y

実験手法

X-RAY DIFFRACTION (1.75 Å)