PDBsum entry 2d80

Hydrolase

PDB id: 2d80

Contents

Protein chain

318 a.a. *

Ligands

NAG-NAG-BMA-MAN-MAN

Waters ×240

* Residue conservation analysis

PDB id:

2d80

Name:

Hydrolase

Title:

Crystal structure of phb depolymerase from penicillium funiculosum

Structure:

Phb depolymerase. Chain: a. Ec: 3.1.1.75

Source:

Penicillium funiculosum. Organism_taxid: 28572. Strain: ifo 6345

Resolution:

1.70Å R-factor: 0.174 R-free: 0.204

Authors:

T.Hisano,K.Kasuya,T.Saito,T.Iwata,K.Miki

Key ref:

T.Hisano et al. (2006). The Crystal Structure of Polyhydroxybutyrate Depolymerase from Penicillium funiculosum Provides Insights into the Recognition and Degradation of Biopolyesters. J Mol Biol, 356, 993. PubMed id: 16405909 DOI: 10.1016/j.jmb.2005.12.028

Date:

30-Nov-05 Release date: 31-Jan-06

Protein chain

B2NHN2  (PHAZ_TALFU) -  Polyhydroxybutyrate depolymerase from Talaromyces funiculosus

Seq: 339 a.a.

Struc: 318 a.a.

Enzyme reactions

• Enzyme class: E.C.3.1.1.75 - poly(3-hydroxybutyrate) depolymerase.
• Reaction:
  1. [(3R)-hydroxybutanoate](n) + H2O = [(3R)-hydroxybutanoate](n-1) + (R)-3-hydroxybutanoate + H⁺
  2. [(3R)-hydroxybutanoate](n) + H2O = [(3R)-hydroxybutanoate](n-2) + (3R)-hydroxybutanoate dimer + H⁺
  3. [(3R)-hydroxybutanoate](n) + H2O = [(3R)-hydroxybutanoate](n-3) + (3R)-hydroxybutanoate trimer + H⁺
  4. [(3R)-hydroxybutanoate](n) + H2O = [(3R)-hydroxybutanoate](n-4) + (3R)-hydroxybutanoate tetramer + H⁺
  5. [(3R)-hydroxybutanoate](n) + H2O = [(3R)-hydroxybutanoate](n-5) + (3R)-hydroxybutanoate pentamer + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

DOI no: 10.1016/j.jmb.2005.12.028

J Mol Biol 356:993 (2006)

PubMed id: 16405909

The Crystal Structure of Polyhydroxybutyrate Depolymerase from Penicillium funiculosum Provides Insights into the Recognition and Degradation of Biopolyesters.

T.Hisano, K.Kasuya, Y.Tezuka, N.Ishii, T.Kobayashi, M.Shiraki, E.Oroudjev, H.Hansma, T.Iwata, Y.Doi, T.Saito, K.Miki.

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 S39A mutant complexed with the methyl ester of a trimer substrate of (R)-3-hydroxybutyrate have been determined at resolutions of 1.71A and 1.66A, 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.

Selected figure(s)

Figure 4.
Figure 4. Simulated-annealing |mF[o] -DF[c]| electron density map for H(R3HB)[3]M bound to the S39A mutant, calculated from the model excluding H(R3HB)[3]M. Models of S39A and the R3HB trimer (H(R3HB)[3]M lacking the methyl group) are also shown as a line and a stick model, respectively. The map is contoured at 3.5s. Figures were produced using the PyMOL program (DeLano, W. L.; http://www.pymol.org/).

Figure 5.
Figure 5. A close-up stereoview of the active site (the S39A-H(R3HB)[3]M complex). Side-chains of catalytic residues and residues forming the substrate-binding site in the crevice are represented as ball-and-stick models. The amide nitrogen atoms of Ser40, Cys250, and Asn302 are also shown. A model of the R3HB trimer (designated as (R3HB)[3]) is also shown as a black ball-and-stick model. A hydrogen bond between Nd1 atom of Trp307 and the carbonyl oxygen of an ester linkage adjacent to a scissile linkage, and one between His155 and Asp121 are indicated as green lines. The side-chain of Ser39 of the wild-type protein (shown in red) is superimposed on Ala39 of the mutant model, and a hydrogen bond between the Og atom of Ser39 and the amide group of Ser40 is tentatively indicated with a green broken line.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 356, 993-0) copyright 2006.

Figures were selected by an automated process.