2D81

PHB depolymerase (S39A) complexed with R3HB trimer

2D81 の概要

• エントリーDOI: 10.2210/pdb2d81/pdb
• 関連するPDBエントリー: 2D80
• 分子名称: PHB depolymerase, 2-acetamido-2-deoxy-beta-D-glucopyranose, (1R)-3-{[(1R)-3-METHOXY-1-METHYL-3-OXOPROPYL]OXY}-1-METHYL-3-OXOPROPYL (3R)-3-HYDROXYBUTANOATE, ... (4 entities in total)
• 機能のキーワード: alpha/beta hydrolase fold, circular permutation, hydrolase
• 由来する生物種: Penicillium funiculosum
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 34021.49

構造登録者

Hisano, T.,Kasuya, K.,Saito, T.,Iwata, T.,Miki, K. (登録日: 2005-11-30, 公開日: 2006-01-31, 最終更新日: 2024-10-09)

主引用文献

Hisano, T.,Kasuya, K.,Tezuka, Y.,Ishii, N.,Kobayashi, T.,Shiraki, M.,Oroudjev, E.,Hansma, H.,Iwata, T.,Doi, Y.,Saito, T.,Miki, K.
The Crystal Structure of Polyhydroxybutyrate Depolymerase from Penicillium funiculosum Provides Insights into the Recognition and Degradation of Biopolyesters
J.Mol.Biol., 356:993-1004, 2006

PubMed Abstract: Polyhydroxybutyrate is a microbial polyester that can be produced from renewable resources, and is degraded by the enzyme polyhydroxybutyrate depolymerase. The crystal structures of polyhydroxybutyrate depolymerase from Penicillium funiculosum and its S39 A mutant complexed with the methyl ester of a trimer substrate of (R)-3-hydroxybutyrate have been determined at resolutions of 1.71 A and 1.66 A, respectively. The enzyme is comprised of a single domain, which represents a circularly permuted variant of the alpha/beta hydrolase fold. The catalytic residues Ser39, Asp121, and His155 are located at topologically conserved positions. The main chain amide groups of Ser40 and Cys250 form an oxyanion hole. A crevice is formed on the surface of the enzyme, to which a single polymer chain can be bound by predominantly hydrophobic interactions with several hydrophobic residues. The structure of the S39A mutant-trimeric substrate complex reveals that Trp307 is responsible for the recognition of the ester group adjacent to the scissile group. It is also revealed that the substrate-binding site includes at least three, and possibly four, subsites for binding monomer units of polyester substrates. Thirteen hydrophobic residues, which are exposed to solvent, are aligned around the mouth of the crevice, forming a putative adsorption site for the polymer surface. These residues may contribute to the sufficient binding affinity of the enzyme for PHB granules without a distinct substrate-binding domain.

PubMed: 16405909
DOI: 10.1016/j.jmb.2005.12.028

実験手法

X-RAY DIFFRACTION (1.66 Å)