5AII

Discovery and characterization of thermophilic limonene-1,2-epoxide hydrolases from hot spring metagenomic libraries. CH55-sample-PEG complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Discovery and Characterization of Thermophilic Limonene-1,2-Epoxide Hydrolases from Hot Spring Metagenomic Libraries

Ferrandi, E.E.Sayer, C.Isupov, M.N.Annovazzi, C.Marchesi, C.Iacobone, G.Peng, X.Bonch-Osmolovskaya, E.Wohlgemuth, R.Littlechild, J.A.Montia, D.

(2015) FEBS J 282: 2879

  • DOI: https://doi.org/10.1111/febs.13328
  • Primary Citation of Related Structures:  
    5AIF, 5AIG, 5AIH, 5AII

  • PubMed Abstract: 

    The epoxide hydrolases (EHs) represent an attractive option for the synthesis of chiral epoxides and 1,2-diols which are valuable building blocks for the synthesis of several pharmaceutical compounds. A metagenomic approach has been used to identify two new members of the atypical EH limonene-1,2-epoxide hydrolase (LEH) family of enzymes. These two LEHs (Tomsk-LEH and CH55-LEH) show EH activities towards different epoxide substrates, differing in most cases from those previously identified for Rhodococcus erythropolis (Re-LEH) in terms of stereoselectivity. Tomsk-LEH and CH55-LEH, both from thermophilic sources, have higher optimal temperatures and apparent melting temperatures than Re-LEH. The new LEH enzymes have been crystallized and their structures solved to high resolution in the native form and in complex with the inhibitor valpromide for Tomsk-LEH and poly(ethylene glycol) for CH55-LEH. The structural analysis has provided insights into the LEH mechanism, substrate specificity and stereoselectivity of these new LEH enzymes, which has been supported by mutagenesis studies.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LIMONENE-1,2-EPOXIDE HYDROLASE
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
135unidentifiedMutation(s): 0 
EC: 3.3.2.8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG6
Query on PG6

Download Ideal Coordinates CCD File 
DC [auth N],
IB [auth I]
1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
C12 H26 O6
DMDPGPKXQDIQQG-UHFFFAOYSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
CC [auth N]
DB [auth H]
EA [auth D]
FB [auth I]
GA [auth D]
CC [auth N],
DB [auth H],
EA [auth D],
FB [auth I],
GA [auth D],
HA [auth D],
HC [auth O],
JB [auth I],
KB [auth J],
KC [auth O],
LC [auth P],
MB [auth K],
NA [auth E],
OA [auth F],
Q [auth A],
RA [auth F],
RB [auth L],
UA [auth G],
V [auth B],
W [auth B],
WA [auth G],
WB [auth M],
Z [auth C],
ZA [auth H]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PG5
Query on PG5

Download Ideal Coordinates CCD File 
U [auth A]1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE
C8 H18 O4
YFNKIDBQEZZDLK-UHFFFAOYSA-N
HIS
Query on HIS

Download Ideal Coordinates CCD File 
TA [auth F]HISTIDINE
C6 H10 N3 O2
HNDVDQJCIGZPNO-YFKPBYRVSA-O
PGE
Query on PGE

Download Ideal Coordinates CCD File 
CA [auth C]
EC [auth N]
FC [auth N]
IA [auth D]
QB [auth K]
CA [auth C],
EC [auth N],
FC [auth N],
IA [auth D],
QB [auth K],
ZB [auth M]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AB [auth H]
FA [auth D]
GB [auth I]
HB [auth I]
IC [auth O]
AB [auth H],
FA [auth D],
GB [auth I],
HB [auth I],
IC [auth O],
JC [auth O],
NB [auth K],
OB [auth K],
PA [auth F],
QA [auth F],
R [auth A],
SB [auth L],
TB [auth L],
X [auth B],
XB [auth M],
Y [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AC [auth M]
BC [auth M]
DA [auth C]
EB [auth H]
GC [auth N]
AC [auth M],
BC [auth M],
DA [auth C],
EB [auth H],
GC [auth N],
JA [auth D],
KA [auth D],
LA [auth D],
MA [auth D],
NC [auth P],
OC [auth P],
PC [auth P],
QC [auth P],
RC [auth P],
SA [auth F],
T [auth A],
VB [auth L],
XA [auth G],
YA [auth G]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
BB [auth H]
CB [auth H]
LB [auth J]
AA [auth C],
BA [auth C],
BB [auth H],
CB [auth H],
LB [auth J],
MC [auth P],
PB [auth K],
S [auth A],
UB [auth L],
VA [auth G],
YB [auth M]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.97α = 90
b = 104.23β = 102.41
c = 148γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-17
    Type: Initial release
  • Version 1.1: 2015-07-22
    Changes: Database references
  • Version 1.2: 2015-08-12
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description