title: The crystal structure of polyhydroxybutyrate depolymerase from Penicillium funiculosum provides insights into the recognition and degradation of biopolyesters.
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.
authors.affiliation: RIKEN Harima Institute/SPring-8, Koto 1-1-1, Mikazuki-cho, Sayo-gun, Hyogo 679-5148, Japan.
authors.forename: Tamao
authors.initials: T
authors.lastname: Hisano
authors.forename: Ken-Ichi
authors.initials: K
authors.lastname: Kasuya
authors.forename: Yoko
authors.initials: Y
authors.lastname: Tezuka
authors.forename: Nariaki
authors.initials: N
authors.lastname: Ishii
authors.forename: Teruyuki
authors.initials: T
authors.lastname: Kobayashi
authors.forename: Mari
authors.initials: M
authors.lastname: Shiraki
authors.forename: Emin
authors.initials: E
authors.lastname: Oroudjev
authors.forename: Helen
authors.initials: H
authors.lastname: Hansma
authors.forename: Tadahisa
authors.initials: T
authors.lastname: Iwata
authors.forename: Yoshiharu
authors.initials: Y
authors.lastname: Doi
authors.forename: Terumi
authors.initials: T
authors.lastname: Saito
authors.forename: Kunio
authors.initials: K
authors.lastname: Miki
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D002265:Carboxylic Ester Hydrolases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D018360:Crystallography, X-Ray; D006885:Hydroxybutyrates / Q000737:chemistry / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D010407:Penicillium / Q000201:enzymology*; D011091:Polyesters / Q000737:chemistry / Q000378:metabolism*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment
chemical_list: D001426:Bacterial Proteins; D006885:Hydroxybutyrates; D011091:Polyesters; D002265:Carboxylic Ester Hydrolases