2D81

PHB depolymerase (S39A) complexed with R3HB trimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

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

(2006) J.Mol.Biol. 356: 993-1004

  • DOI: 10.1016/j.jmb.2005.12.028
  • Primary Citation of Related Structures:  

  • 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 it ...

    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.


    Organizational Affiliation

    RIKEN Harima Institute/SPring-8, Koto 1-1-1, Mikazuki-cho, Sayo-gun, Hyogo 679-5148, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHB depolymerase
A
318Talaromyces funiculosusMutation(s): 0 
Gene Names: phaZPfu
Find proteins for B2NHN2 (Talaromyces funiculosus)
Go to UniProtKB:  B2NHN2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RB3
Query on RB3

Download SDF File 
Download CCD File 
A
(1R)-3-{[(1R)-3-METHOXY-1-METHYL-3-OXOPROPYL]OXY}-1-METHYL-3-OXOPROPYL (3R)-3-HYDROXYBUTANOATE
METHYL (3R)-3-{[(3R)-3-{[(3R)-3-HYDROXYBUTANOYL]OXY}BUTANOYL]OXY}BUTANOATE
C13 H22 O7
WGAHBMKAEWUQKL-OPRDCNLKSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.176 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 81.934α = 90.00
b = 48.863β = 94.45
c = 64.198γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
MOLREPphasing
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-31
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance