8B4U | pdb_00008b4u

The crystal structure of PET46, a PETase enzyme from Candidatus bathyarchaeota


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 
    0.173 (Depositor), 0.173 (DCC) 
  • R-Value Work: 
    0.152 (Depositor), 0.153 (DCC) 
  • R-Value Observed: 
    0.153 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 8B4U

This is version 1.3 of the entry. See complete history

Literature

An archaeal lid-containing feruloyl esterase degrades polyethylene terephthalate.

Perez-Garcia, P.Chow, J.Costanzi, E.Gurschke, M.Dittrich, J.Dierkes, R.F.Molitor, R.Applegate, V.Feuerriegel, G.Tete, P.Danso, D.Thies, S.Schumacher, J.Pfleger, C.Jaeger, K.E.Gohlke, H.Smits, S.H.J.Schmitz, R.A.Streit, W.R.

(2023) Commun Chem 6: 193-193

  • DOI: https://doi.org/10.1038/s42004-023-00998-z
  • Primary Citation Related Structures: 
    8B4U

  • PubMed Abstract: 

    Polyethylene terephthalate (PET) is a commodity polymer known to globally contaminate marine and terrestrial environments. Today, around 80 bacterial and fungal PET-active enzymes (PETases) are known, originating from four bacterial and two fungal phyla. In contrast, no archaeal enzyme had been identified to degrade PET. Here we report on the structural and biochemical characterization of PET46 (RLI42440.1), an archaeal promiscuous feruloyl esterase exhibiting degradation activity on semi-crystalline PET powder comparable to IsPETase and LCC (wildtypes), and higher activity on bis-, and mono-(2-hydroxyethyl) terephthalate (BHET and MHET). The enzyme, found by a sequence-based metagenome search, is derived from a non-cultivated, deep-sea Candidatus Bathyarchaeota archaeon. Biochemical characterization demonstrated that PET46 is a promiscuous, heat-adapted hydrolase. Its crystal structure was solved at a resolution of 1.71 Å. It shares the core alpha/beta-hydrolase fold with bacterial PETases, but contains a unique lid common in feruloyl esterases, which is involved in substrate binding. Thus, our study widens the currently known diversity of PET-hydrolyzing enzymes, by demonstrating PET depolymerization by a plant cell wall-degrading esterase.


  • Organizational Affiliation
    • Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 32.87 kDa 
  • Atom Count: 2,480 
  • Modeled Residue Count: 269 
  • Deposited Residue Count: 277 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha/beta hydrolase277Candidatus Bathyarchaeota archaeonMutation(s): 0 
Gene Names: DRO64_06360
UniProt
Find proteins for A0ACD6BAI4 (Candidatus Bathyarchaeota archaeon)
Explore A0ACD6BAI4 
Go to UniProtKB:  A0ACD6BAI4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6BAI4
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4

Query on PO4



Download:Ideal Coordinates CCD File
V [auth A],
W [auth A],
X [auth A],
Y [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO

Query on EDO



Download:Ideal Coordinates CCD File
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
Z [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free:  0.173 (Depositor), 0.173 (DCC) 
  • R-Value Work:  0.152 (Depositor), 0.153 (DCC) 
  • R-Value Observed: 0.153 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.292α = 90
b = 79.292β = 90
c = 171.546γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany417919780
German Federal Ministry for Education and ResearchGermany31B0837A

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-23
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Structure summary
  • Version 1.3: 2026-03-04
    Changes: Refinement description