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 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 

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Ligand Structure Quality Assessment 


This is version 1.2 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: 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 ...

    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

    Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Straße 15, 12489, Berlin, Germany. gert.weber@helmholtz-berlin.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mono(2-hydroxyethyl) terephthalate hydrolase
A, B, C, D, E, F
A, B, C, D, E, F
596Ideonella sakaiensisMutation(s): 0 
Gene Names: ISF6_0224
EC: 3.1.1.102
UniProt
Find proteins for A0A0K8P8E7 (Ideonella sakaiensis (strain NBRC 110686 / TISTR 2288 / 201-F6))
Explore A0A0K8P8E7 
Go to UniProtKB:  A0A0K8P8E7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0K8P8E7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / 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],
AA [auth E],
BA [auth E],
CA [auth E],
G [auth A],
GA [auth F],
HA [auth F],
M [auth B],
T [auth C],
U [auth C],
Y [auth D]
4-(2-hydroxyethylcarbamoyl)benzoic acid
C10 H11 N O4
HGTVOBHNUAVYMK-UHFFFAOYSA-N
 Ligand Interaction
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
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
DA [auth E],
H [auth A],
I [auth A],
IA [auth F],
J [auth A],
DA [auth E],
H [auth A],
I [auth A],
IA [auth F],
J [auth A],
JA [auth F],
KA [auth F],
N [auth B],
O [auth B],
P [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
EA [auth E],
L [auth A],
LA [auth F],
R [auth B],
V [auth C],
EA [auth E],
L [auth A],
LA [auth F],
R [auth B],
V [auth C],
Z [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 
  • 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

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Ligand Structure Quality Assessment 


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