6QGA

Crystal structure of Ideonella sakaiensis MHETase bound to the non-hydrolyzable ligand MHETA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.198 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.4 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
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
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
J1K
Query on J1K

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
CA [auth E]
G [auth A]
GA [auth F]
4-(2-hydroxyethylcarbamoyl)benzoic acid
C10 H11 N O4
HGTVOBHNUAVYMK-UHFFFAOYSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
K [auth A],
Q [auth B]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
DA [auth E]
H [auth A]
I [auth A]
IA [auth F]
J [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CA
Query on CA

Download Ideal Coordinates CCD File 
EA [auth E]
L [auth A]
LA [auth F]
R [auth B]
V [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
FA [auth E],
S [auth B],
W [auth C],
X [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.198 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.153α = 90
b = 183.646β = 90
c = 246.752γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MoRDaphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted J1KClick on this verticalbar to view details

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: Advisory, Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary