1WN3

Crystal structure of TT0310 protein from Thermus thermophilus HB8

Summary for 1WN3

• Entry DOI: 10.2210/pdb1wn3/pdb
• Related: 1WLU 1WLV
• Descriptor: phenylacetic acid degradation protein PaaI, CHLORIDE ION, HEXANOYL-COENZYME A, ... (5 entities in total)
• Functional Keywords: thioesterase, hot dog fold, phenylacetic acid degradation, structural genomics, riken structural genomics/proteomics initiative, rsgi, unknown function
• Biological source: Thermus thermophilus HB8
• Total number of polymer chains: 8
• Total formula weight: 117834.45

Authors

Kunishima, N.,Sugahara, M.,Miyano, M.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2004-07-27, release date: 2005-07-05, Last modification date: 2023-10-25)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (2.1 Å)