6QG9

Crystal structure of Ideonella sakaiensis MHETase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the plastic-degrading Ideonella sakaiensis MHETase bound to a substrate.

Palm, G.J.Reisky, L.Bottcher, D.Muller, H.Michels, E.A.P.Walczak, M.C.Berndt, L.Weiss, M.S.Bornscheuer, U.T.Weber, G.

(2019) Nat Commun 10: 1717-1717

  • DOI: https://doi.org/10.1038/s41467-019-09326-3
  • Primary Citation of Related Structures:  
    6QG9, 6QGA, 6QGB, 6QGC

  • PubMed Abstract: 

    The extreme durability of polyethylene terephthalate (PET) debris has rendered it a long-term environmental burden. At the same time, current recycling efforts still lack sustainability. Two recently discovered bacterial enzymes that specifically degrade PET represent a promising solution. First, Ideonella sakaiensis PETase, a structurally well-characterized consensus α/β-hydrolase fold enzyme, converts PET to mono-(2-hydroxyethyl) terephthalate (MHET). MHETase, the second key enzyme, hydrolyzes MHET to the PET educts terephthalate and ethylene glycol. Here, we report the crystal structures of active ligand-free MHETase and MHETase bound to a nonhydrolyzable MHET analog. MHETase, which is reminiscent of feruloyl esterases, possesses a classic α/β-hydrolase domain and a lid domain conferring substrate specificity. In the light of structure-based mapping of the active site, activity assays, mutagenesis studies and a first structure-guided alteration of substrate specificity towards bis-(2-hydroxyethyl) terephthalate (BHET) reported here, we anticipate MHETase to be a valuable resource to further advance enzymatic plastic degradation.


  • Organizational Affiliation

    Molecular Structural Biology, University of Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mono(2-hydroxyethyl) terephthalate hydrolase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
596Piscinibacter sakaiensisMutation(s): 0 
Gene Names: ISF6_0224
EC: 3.1.1.102
UniProt
Find proteins for A0A0K8P8E7 (Piscinibacter sakaiensis)
Explore A0A0K8P8E7 
Go to UniProtKB:  A0A0K8P8E7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0K8P8E7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth F]
CA [auth G]
EA [auth H]
GA [auth I]
M [auth A]
AA [auth F],
CA [auth G],
EA [auth H],
GA [auth I],
M [auth A],
N [auth A],
P [auth B],
R [auth C],
U [auth D],
W [auth E],
X [auth E]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
K [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
S [auth D],
Y [auth F]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA
Query on CA

Download Ideal Coordinates CCD File 
BA [auth G]
DA [auth H]
FA [auth I]
HA [auth J]
L [auth A]
BA [auth G],
DA [auth H],
FA [auth I],
HA [auth J],
L [auth A],
O [auth B],
Q [auth C],
T [auth D],
V [auth E],
Z [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.286α = 83.01
b = 137.949β = 66.88
c = 137.051γ = 68.45
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Data collection, Structure summary
  • Version 1.2: 2019-04-24
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description