1J1Y

Crystal Structure of PaaI from Thermus thermophilus HB8

1J1Y の概要

• エントリーDOI: 10.2210/pdb1j1y/pdb
• 分子名称: PaaI protein, CHLORIDE ION, MAGNESIUM ION, ... (4 entities in total)
• 機能のキーワード: thioesterase, hot dog fold, phenylacetic acid degradation, structural genomics, riken structural genomics/proteomics initiative, rsgi, hydrolase
• 由来する生物種: Thermus thermophilus
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 28620.21

構造登録者

Kunishima, N.,Sugahara, M.,Kuramitsu, S.,Yokoyama, S.,Miyano, M.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (登録日: 2002-12-24, 公開日: 2004-02-17, 最終更新日: 2023-12-27)

主引用文献

Kunishima, N.,Asada, Y.,Sugahara, M.,Ishijima, J.,Nodake, Y.,Sugahara, M.,Miyano, M.,Kuramitsu, S.,Yokoyama, S.,Sugahara, M.
A Novel Induced-fit Reaction Mechanism of Asymmetric Hot Dog Thioesterase PaaI
J.Mol.Biol., 352:212-228, 2005

PubMed Abstract: Hot dog fold proteins sharing the characteristic "hot dog" fold are known to involve certain coenzyme A binding enzymes with various oligomeric states. In order to elucidate the oligomerization-function relationship of the hot dog fold proteins, crystal structures of the phenylacetate degradation protein PaaI from Thermus thermophilus HB8 (TtPaaI), a tetrameric acyl-CoA thioesterase with the hot dog fold, have been determined and compared with those of other family members. In the liganded crystal forms with coenzyme A derivatives, only two of four intersubunit catalytic pockets of the TtPaaI tetramer are occupied by the ligands. A detailed structural comparison between several liganded and unliganded forms reveals that a subtle rigid-body rearrangement of subunits within 2 degrees upon binding of the first two ligand molecules can induce a strict negative cooperativity to prevent further binding at the remaining two pockets, indicating that the so-called "half-of-the-sites reactivity" of oligomeric enzymes is visualized for the first time. Considering kinetic and mutational analyses together, a possible reaction mechanism of TtPaaI is proposed; one tetramer binds only two acyl-CoA molecules with a novel asymmetric induced-fit mechanism and carries out the hydrolysis according to a base-catalyzed reaction through activation of a water molecule by Asp48. From a structural comparison with other family members, it is concluded that a subgroup of the hot dog fold protein family, referred to as "asymmetric hot dog thioesterases" including medium chain acyl-CoA thioesterase II from Escherichia coli and human thioesterase III, might share the same oligomerization mode and the asymmetric induced-fit mechanism as observed in TtPaaI.

PubMed: 16061252
DOI: 10.1016/j.jmb.2005.07.008

実験手法

X-RAY DIFFRACTION (1.7 Å)