1WYU

Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in holo form

1WYU の概要

• エントリーDOI: 10.2210/pdb1wyu/pdb
• 関連するPDBエントリー: 1WYT 1WYV
• 分子名称: glycine dehydrogenase (decarboxylating) subunit 1, glycine dehydrogenase subunit 2 (P-protein), PYRIDOXAL-5'-PHOSPHATE, ... (4 entities in total)
• 機能のキーワード: alpha(2)beta(2) tetramer, riken structural genomics/proteomics initiative, rsgi, structural genomics, oxidoreductase
• 由来する生物種: Thermus thermophilus; 詳細
• タンパク質・核酸の鎖数: 8
• 化学式量合計: 400799.94

構造登録者

Nakai, T.,Nakagawa, N.,Maoka, N.,Masui, R.,Kuramitsu, S.,Kamiya, N.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (登録日: 2005-02-17, 公開日: 2005-04-05, 最終更新日: 2025-03-26)

主引用文献

Nakai, T.,Nakagawa, N.,Maoka, N.,Masui, R.,Kuramitsu, S.,Kamiya, N.
Structure of P-protein of the glycine cleavage system: implications for nonketotic hyperglycinemia
Embo J., 24:1523-1536, 2005

PubMed Abstract: The crystal structure of the P-protein of the glycine cleavage system from Thermus thermophilus HB8 has been determined. This is the first reported crystal structure of a P-protein, and it reveals that P-proteins do not involve the alpha(2)-type active dimer universally observed in the evolutionarily related pyridoxal 5'-phosphate (PLP)-dependent enzymes. Instead, novel alphabeta-type dimers associate to form an alpha(2)beta(2) tetramer, where the alpha- and beta-subunits are structurally similar and appear to have arisen by gene duplication and subsequent divergence with a loss of one active site. The binding of PLP to the apoenzyme induces large open-closed conformational changes, with residues moving up to 13.5 A. The structure of the complex formed by the holoenzyme bound to an inhibitor, (aminooxy)acetate, suggests residues that may be responsible for substrate recognition. The molecular surface around the lipoamide-binding channel shows conservation of positively charged residues, which are possibly involved in complex formation with the H-protein. These results provide insights into the molecular basis of nonketotic hyperglycinemia.

PubMed: 15791207
DOI: 10.1038/sj.emboj.7600632

実験手法

X-RAY DIFFRACTION (2.1 Å)