5NG7

Novel epoxide hydrolases belonging to the alpha/beta hydrolases superfamily in metagenomes from hot environments


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

New Thermophilic alpha / beta Class Epoxide Hydrolases Found in Metagenomes From Hot Environments.

Ferrandi, E.E.Sayer, C.De Rose, S.A.Guazzelli, E.Marchesi, C.Saneei, V.Isupov, M.N.Littlechild, J.A.Monti, D.

(2018) Front Bioeng Biotechnol 6: 144-144

  • DOI: https://doi.org/10.3389/fbioe.2018.00144
  • Primary Citation of Related Structures:  
    5NFQ, 5NG7

  • PubMed Abstract: 

    Two novel epoxide hydrolases (EHs), Sibe-EH and CH65-EH, were identified in the metagenomes of samples collected in hot springs in Russia and China, respectively. The two α/β hydrolase superfamily fold enzymes were cloned, over-expressed in Escherichia coli , purified and characterized. The new EHs were active toward a broad range of substrates, and in particular, Sibe-EH was excellent in the desymmetrization of cis -2,3-epoxybutane producing the (2 R ,3 R )-diol product with ee exceeding 99%. Interestingly these enzymes also hydrolyse (4 R )-limonene-1,2-epoxide with Sibe-EH being specific for the trans isomer. The Sibe-EH is a monomer in solution whereas the CH65-EH is a dimer. Both enzymes showed high melting temperatures with the CH65-EH being the highest at 85°C retaining 80% of its initial activity after 3 h thermal treatment at 70°C making it the most thermal tolerant wild type epoxide hydrolase described. The Sibe-EH and CH65-EH have been crystallized and their structures determined to high resolution, 1.6 and 1.4 Å, respectively. The CH65-EH enzyme forms a dimer via its cap domains with different relative orientation of the monomers compared to previously described EHs. The entrance to the active site cavity is located in a different position in CH65-EH and Sibe-EH in relation to other known bacterial and mammalian EHs.


  • Organizational Affiliation

    Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Milan, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
epoxide hydrolase
A, B
299metagenomeMutation(s): 0 
EC: 3.3.2.10
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
J [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SER
Query on SER

Download Ideal Coordinates CCD File 
H [auth B]SERINE
C3 H7 N O3
MTCFGRXMJLQNBG-REOHCLBHSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
I [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B],
G [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 163.94α = 90
b = 46.22β = 106.94
c = 73.87γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
xia2data reduction
Aimlessdata scaling
MoRDaphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European UnionUnited KingdomFP7/2007-2013 HOTZYME

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2018-11-14
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description