7U1V

Structure of SPAC806.04c protein from fission yeast covalently bound to BeF3

7U1V の概要

• エントリーDOI: 10.2210/pdb7u1v/pdb
• 関連するPDBエントリー: 7T7K 7T7O
• 分子名称: Damage-control phosphatase SPAC806.04c, NICKEL (II) ION, PHOSPHATE ION, ... (5 entities in total)
• 機能のキーワード: metal-dependent phosphatase, domain of unknown function 89 (duf89), hydrolase
• 由来する生物種: Schizosaccharomyces pombe (fission yeast)
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 100513.62

構造登録者

Jacewicz, A.,Sanchez, A.M.,Shuman, S. (登録日: 2022-02-22, 公開日: 2022-06-01, 最終更新日: 2024-11-06)

主引用文献

Sanchez, A.M.,Jacewicz, A.,Shuman, S.
Fission yeast Duf89 and Duf8901 are cobalt/nickel-dependent phosphatase-pyrophosphatases that act via a covalent aspartyl-phosphate intermediate.
J.Biol.Chem., 298:101851-101851, 2022

PubMed Abstract: Domain of Unknown Function 89 (DUF89) proteins are metal-dependent phosphohydrolases. Exemplary DUF89 enzymes differ in their metal and phosphosubstrate preferences. Here, we interrogated the activities and structures of two DUF89 paralogs from fission yeast-Duf89 and Duf8901. We find that Duf89 and Duf8901 are cobalt/nickel-dependent phosphohydrolases adept at hydrolyzing p-nitrophenylphosphate and PP. Crystal structures of metal-free Duf89 and Co-bound Duf8901 disclosed two enzyme conformations that differed with respect to the position of a three-helix module, which is either oriented away from the active site in Duf89 or forms a lid over the active site in Duf8901. Lid closure results in a 16 Å movement of Duf8901 Asp195, vis-à-vis Asp199 in Duf89, that brings Asp195 into contact with an octahedrally coordinated cobalt. Reaction of Duf8901 with BeCl and NaF in the presence of divalent cations Co, Ni, or Zn generated covalent Duf8901-(Asp248)-beryllium trifluoride (BeF)•Co, Duf8901-(Asp248)-BeF•Ni, or Duf8901-(Asp248)-BeF•Zn adducts, the structures of which suggest a two-step catalytic mechanism via formation and hydrolysis of an enzyme-(aspartyl)-phosphate intermediate. Alanine mutations of Duf8901 Asp248, Asn249, Lys401, Asp286, and Asp195 that interact with BeF•Co squelched p-nitrophenylphosphatase activity. A 1.8 Å structure of a Duf8901-(Asp248)-AlF-OH•Co transition-state mimetic suggests an associative mechanism in which Asp195 and Asp363 orient and activate the water nucleophile. Whereas deletion of the duf89 gene elicited a phenotype in which expression of phosphate homeostasis gene pho1 was derepressed, deleting duf8901 did not, thereby hinting that the DUF89 paralogs have distinct functional repertoires in vivo.

PubMed: 35314193
DOI: 10.1016/j.jbc.2022.101851

実験手法

X-RAY DIFFRACTION (2.1 Å)