7Z6B

PET hydrolase PET6 from halophilic organsim Vibrio gazogenes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.126 
  • R-Value Work: 0.100 
  • R-Value Observed: 0.101 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Investigation of the halophilic PET hydrolase PET6 from Vibrio gazogenes.

Weigert, S.Perez-Garcia, P.Gisdon, F.J.Gagsteiger, A.Schweinshaut, K.Ullmann, G.M.Chow, J.Streit, W.R.Hocker, B.

(2022) Protein Sci 31: e4500-e4500

  • DOI: https://doi.org/10.1002/pro.4500

  • PubMed Abstract: 

    The handling of plastic waste and the associated ubiquitous occurrence of microplastic poses one of the biggest challenges of our time. Recent investigations of plastic degrading enzymes have opened new prospects for biological microplastic decomposition as well as recycling applications. For polyethylene terephthalate, in particular, several natural and engineered enzymes are known to have such promising properties. From a previous study that identified new PETase candidates by homology search, we chose the candidate PET6 from the globally distributed, halophilic organism Vibrio gazogenes for further investigation. By mapping the occurrence of Vibrios containing PET6 homologs we demonstrated their ubiquitous prevalence in the pangenome of several Vibrio strains. The biochemical characterization of PET6 showed that PET6 has a comparatively lower activity than other enzymes but also revealed a superior turnover at very high salt concentrations. The crystal structure of PET6 provides structural insights into this adaptation to saline environments. By grafting only a few beneficial mutations from other PET degrading enzymes onto PET6, we increased the activity up to three-fold, demonstrating the evolutionary potential of the enzyme. MD simulations of the variant helped rationalize the mutational effects of those mutants and elucidate the interaction of the enzyme with a PET substrate. With tremendous amounts of plastic waste in the Ocean and the prevalence of Vibrio gazogenes in marine biofilms and estuarine marshes, our findings suggest that Vibrio and the PET6 enzyme are worthy subjects to study the PET degradation in marine environments.


  • Organizational Affiliation

    Department of Biochemistry, University of Bayreuth, Bayreuth, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cutinase
A, B, C
295Vibrio gazogenes DSM 21264 = NBRC 103151Mutation(s): 0 
Gene Names: SAMN02745781_03338
UniProt
Find proteins for A0A1M5F0K3 (Vibrio gazogenes DSM 21264 = NBRC 103151)
Explore A0A1M5F0K3 
Go to UniProtKB:  A0A1M5F0K3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1M5F0K3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
IA [auth C]
JA [auth C]
AA [auth B],
BA [auth B],
CA [auth B],
IA [auth C],
JA [auth C],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
X [auth B],
Y [auth B],
Z [auth B]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
G [auth A]
GA [auth C]
H [auth A]
HA [auth C]
I [auth A]
G [auth A],
GA [auth C],
H [auth A],
HA [auth C],
I [auth A],
J [auth A],
U [auth B],
V [auth B],
W [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A],
DA [auth C],
R [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A]
EA [auth C]
F [auth A]
FA [auth C]
S [auth B]
E [auth A],
EA [auth C],
F [auth A],
FA [auth C],
S [auth B],
T [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.126 
  • R-Value Work: 0.100 
  • R-Value Observed: 0.101 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.82α = 119.779
b = 72.61β = 91.64
c = 72.76γ = 91.824
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany391977956
German Federal Ministry for Education and ResearchGermany031B0562A, 031B0837B, 031B867B and 031B0571A

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-23
    Type: Initial release
  • Version 1.1: 2022-12-07
    Changes: Database references
  • Version 1.2: 2022-12-14
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description