2ZOD

Crystal structure of selenophosphate synthetase from Aquifex aeolicus

「2YYD」から置き換えられました

2ZOD の概要

• エントリーDOI: 10.2210/pdb2zod/pdb
• 関連するPDBエントリー: 2YYE 2ZAU
• 分子名称: Selenide, water dikinase, SULFATE ION (3 entities in total)
• 機能のキーワード: full-length selenophosphate synthetase, transferase, atp-binding, kinase, magnesium, nucleotide-binding, selenium, selenocysteine, structural genomics, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi
• 由来する生物種: Aquifex aeolicus
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 75586.74

構造登録者

Sekine, S.I.,Matsumoto, E.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (登録日: 2008-05-09, 公開日: 2008-05-27, 最終更新日: 2023-11-01)

主引用文献

Itoh, Y.,Sekine, S.,Matsumoto, E.,Akasaka, R.,Takemoto, C.,Shirouzu, M.,Yokoyama, S.
Structure of selenophosphate synthetase essential for selenium incorporation into proteins and RNAs.
J.Mol.Biol., 385:1456-1469, 2009

PubMed Abstract: Selenophosphate synthetase (SPS) catalyzes the activation of selenide with adenosine 5'-triphosphate (ATP) to generate selenophosphate, the essential reactive selenium donor for the formation of selenocysteine (Sec) and 2-selenouridine residues in proteins and RNAs, respectively. Many SPS are themselves Sec-containing proteins, in which Sec replaces Cys in the catalytically essential position (Sec/Cys). We solved the crystal structures of Aquifex aeolicus SPS and its complex with adenosine 5'-(alpha,beta-methylene) triphosphate (AMPCPP). The ATP-binding site is formed at the subunit interface of the homodimer. Four Asp residues coordinate four metal ions to bind the phosphate groups of AMPCPP. In the free SPS structure, the two loop regions in the ATP-binding site are not ordered, and no enzyme-associated metal is observed. This suggests that ATP binding, metal binding, and the formation of their binding sites are interdependent. To identify the amino-acid residues that contribute to SPS activity, we prepared six mutants of SPS and examined their selenide-dependent ATP consumption. Mutational analyses revealed that Sec/Cys13 and Lys16 are essential. In SPS.AMPCPP, the N-terminal loop, including the two residues, assumes different conformations ("open" and "closed") between the two subunits. The AMPCPP gamma-phosphate group is solvent-accessible, suggesting that a putative nucleophile could attack the ATP gamma-phosphate group to generate selenophosphate and adenosine 5'-diphosphate (ADP). Selenide attached to Sec/Cys13 as -Se-Se(-)/-S-Se(-) could serve as the nucleophile in the "closed" conformation. A water molecule, fixed close to the beta-phosphate group, could function as the nucleophile in subsequent ADP hydrolysis to orthophosphate and adenosine 5'-monophosphate.

PubMed: 18773910
DOI: 10.1016/j.jmb.2008.08.042

実験手法

X-RAY DIFFRACTION (1.98 Å)