7VMD | pdb_00007vmd

Crystal structure of a hydrolases Ple628 from marine microbial consortium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 
    0.186 (Depositor), 0.192 (DCC) 
  • R-Value Work: 
    0.154 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 
    0.156 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Molecular and Biochemical Differences of the Tandem and Cold-Adapted PET Hydrolases Ple628 and Ple629, Isolated From a Marine Microbial Consortium.

Meyer Cifuentes, I.E.Wu, P.Zhao, Y.Liu, W.Neumann-Schaal, M.Pfaff, L.Barys, J.Li, Z.Gao, J.Han, X.Bornscheuer, U.T.Wei, R.Ozturk, B.

(2022) Front Bioeng Biotechnol 10: 930140-930140

  • DOI: https://doi.org/10.3389/fbioe.2022.930140
  • Primary Citation Related Structures: 
    7VMD, 7VPA

  • PubMed Abstract: 

    Polybutylene adipate terephthalate (PBAT) is a biodegradable alternative to polyethylene and can be broadly used in various applications. These polymers can be degraded by hydrolases of terrestrial and aquatic origin. In a previous study, we identified tandem PETase-like hydrolases (Ples) from the marine microbial consortium I1 that were highly expressed when a PBAT blend was supplied as the only carbon source. In this study, the tandem Ples, Ple628 and Ple629, were recombinantly expressed and characterized. Both enzymes are mesophilic and active on a wide range of oligomers. The activities of the Ples differed greatly when model substrates, PBAT-modified polymers or PET nanoparticles were supplied. Ple629 was always more active than Ple628. Crystal structures of Ple628 and Ple629 revealed a structural similarity to other PETases and can be classified as member of the PETases IIa subclass, α/β hydrolase superfamily. Our results show that the predicted functions of Ple628 and Ple629 agree with the bioinformatic predictions, and these enzymes play a significant role in the plastic degradation by the consortium.


  • Organizational Affiliation
    • Junior Research Group Microbial Biotechnology, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.

Macromolecule Content 

  • Total Structure Weight: 31.31 kDa 
  • Atom Count: 2,391 
  • Modeled Residue Count: 266 
  • Deposited Residue Count: 293 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
hydrolase Ple628293unclassified MarinobacterMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free:  0.186 (Depositor), 0.192 (DCC) 
  • R-Value Work:  0.154 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 0.156 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.733α = 90
b = 64.54β = 90
c = 81.409γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-24
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-11-06
    Changes: Structure summary