5AII | pdb_00005aii

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

PDB DOI: https://doi.org/10.2210/pdb5AII/pdb

Classification: HYDROLASE
Organism(s): unidentified
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-02-13 Released: 2015-06-17
Deposition Author(s): Ferrandi, E., Sayer, C., Isupov, M.N., Annovazzi, C., Marchesi, C., Iacobone, G., Peng, X., Bonch-Osmolovskaya, E., Wohlgemuth, R., Littlechild, J.A., Montia, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free:
0.208 (Depositor), 0.208 (DCC)
R-Value Work:
0.175 (Depositor), 0.175 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

PubMed: 26032250 Search on PubMed
DOI: https://doi.org/10.1111/febs.13328
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 244.19 kDa
Atom Count: 18,828
Modeled Residue Count: 2,013
Deposited Residue Count: 2,160
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
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	135	unidentified	Mutation(s): 0 EC: 3.3.2.8

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG6 Query on PG6 Download:Ideal Coordinates CCD File SDF format, chain IB [auth I] SDF format, chain DC [auth N] MOL2 format, chain IB [auth I] MOL2 format, chain DC [auth N] mmCIF format, chain IB [auth I] mmCIF format, chain DC [auth N]	DC [auth N], IB [auth I]	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE C₁₂ H₂₆ O₆ DMDPGPKXQDIQQG-UHFFFAOYSA-N		Interactions Focus chain DC [auth N] Focus chain IB [auth I] Interactions & Density Focus chain DC [auth N] Focus chain IB [auth I]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain ZA [auth H] SDF format, chain Z [auth C] SDF format, chain WB [auth M] SDF format, chain WA [auth G] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain UA [auth G] SDF format, chain RB [auth L] SDF format, chain RA [auth F] SDF format, chain Q [auth A] SDF format, chain OA [auth F] SDF format, chain NA [auth E] SDF format, chain MB [auth K] SDF format, chain LC [auth P] SDF format, chain KC [auth O] SDF format, chain KB [auth J] SDF format, chain JB [auth I] SDF format, chain HC [auth O] SDF format, chain HA [auth D] SDF format, chain GA [auth D] SDF format, chain FB [auth I] SDF format, chain EA [auth D] SDF format, chain DB [auth H] SDF format, chain CC [auth N] MOL2 format, chain ZA [auth H] MOL2 format, chain Z [auth C] MOL2 format, chain WB [auth M] MOL2 format, chain WA [auth G] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain UA [auth G] MOL2 format, chain RB [auth L] MOL2 format, chain RA [auth F] MOL2 format, chain Q [auth A] MOL2 format, chain OA [auth F] MOL2 format, chain NA [auth E] MOL2 format, chain MB [auth K] MOL2 format, chain LC [auth P] MOL2 format, chain KC [auth O] MOL2 format, chain KB [auth J] MOL2 format, chain JB [auth I] MOL2 format, chain HC [auth O] MOL2 format, chain HA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain FB [auth I] MOL2 format, chain EA [auth D] MOL2 format, chain DB [auth H] MOL2 format, chain CC [auth N] mmCIF format, chain ZA [auth H] mmCIF format, chain Z [auth C] mmCIF format, chain WB [auth M] mmCIF format, chain WA [auth G] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain UA [auth G] mmCIF format, chain RB [auth L] mmCIF format, chain RA [auth F] mmCIF format, chain Q [auth A] mmCIF format, chain OA [auth F] mmCIF format, chain NA [auth E] mmCIF format, chain MB [auth K] mmCIF format, chain LC [auth P] mmCIF format, chain KC [auth O] mmCIF format, chain KB [auth J] mmCIF format, chain JB [auth I] mmCIF format, chain HC [auth O] mmCIF format, chain HA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain FB [auth I] mmCIF format, chain EA [auth D] mmCIF format, chain DB [auth H] mmCIF format, chain CC [auth N]	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		Interactions Focus chain CC [auth N] Focus chain DB [auth H] Focus chain EA [auth D] Focus chain FB [auth I] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain HC [auth O] Focus chain JB [auth I] Focus chain KB [auth J] Focus chain KC [auth O] Focus chain LC [auth P] Focus chain MB [auth K] Focus chain NA [auth E] Focus chain OA [auth F] Focus chain Q [auth A] Focus chain RA [auth F] Focus chain RB [auth L] Focus chain UA [auth G] Focus chain V [auth B] Focus chain W [auth B] Focus chain WA [auth G] Focus chain WB [auth M] Focus chain Z [auth C] Focus chain ZA [auth H] Interactions & Density Focus chain CC [auth N] Focus chain DB [auth H] Focus chain EA [auth D] Focus chain FB [auth I] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain HC [auth O] Focus chain JB [auth I] Focus chain KB [auth J] Focus chain KC [auth O] Focus chain LC [auth P] Focus chain MB [auth K] Focus chain NA [auth E] Focus chain OA [auth F] Focus chain Q [auth A] Focus chain RA [auth F] Focus chain RB [auth L] Focus chain UA [auth G] Focus chain V [auth B] Focus chain W [auth B] Focus chain WA [auth G] Focus chain WB [auth M] Focus chain Z [auth C] Focus chain ZA [auth H]
PG5 Query on PG5 Download:Ideal Coordinates CCD File SDF format, chain U [auth A] MOL2 format, chain U [auth A] mmCIF format, chain U [auth A]	U [auth A]	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE C₈ H₁₈ O₄ YFNKIDBQEZZDLK-UHFFFAOYSA-N		Interactions Focus chain U [auth A] Interactions & Density Focus chain U [auth A]
HIS Query on HIS Download:Ideal Coordinates CCD File SDF format, chain TA [auth F] MOL2 format, chain TA [auth F] mmCIF format, chain TA [auth F]	TA [auth F]	HISTIDINE C₆ H₁₀ N₃ O₂ HNDVDQJCIGZPNO-YFKPBYRVSA-O		Interactions Focus chain TA [auth F] Interactions & Density Focus chain TA [auth F]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain ZB [auth M] SDF format, chain QB [auth K] SDF format, chain IA [auth D] SDF format, chain FC [auth N] SDF format, chain EC [auth N] SDF format, chain CA [auth C] MOL2 format, chain ZB [auth M] MOL2 format, chain QB [auth K] MOL2 format, chain IA [auth D] MOL2 format, chain FC [auth N] MOL2 format, chain EC [auth N] MOL2 format, chain CA [auth C] mmCIF format, chain ZB [auth M] mmCIF format, chain QB [auth K] mmCIF format, chain IA [auth D] mmCIF format, chain FC [auth N] mmCIF format, chain EC [auth N] mmCIF format, chain CA [auth C]	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		Interactions Focus chain CA [auth C] Focus chain EC [auth N] Focus chain FC [auth N] Focus chain IA [auth D] Focus chain QB [auth K] Focus chain ZB [auth M] Interactions & Density Focus chain CA [auth C] Focus chain EC [auth N] Focus chain FC [auth N] Focus chain IA [auth D] Focus chain QB [auth K] Focus chain ZB [auth M]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain XB [auth M] SDF format, chain X [auth B] SDF format, chain TB [auth L] SDF format, chain SB [auth L] SDF format, chain R [auth A] SDF format, chain QA [auth F] SDF format, chain PA [auth F] SDF format, chain OB [auth K] SDF format, chain NB [auth K] SDF format, chain JC [auth O] SDF format, chain IC [auth O] SDF format, chain HB [auth I] SDF format, chain GB [auth I] SDF format, chain FA [auth D] SDF format, chain AB [auth H] MOL2 format, chain Y [auth B] MOL2 format, chain XB [auth M] MOL2 format, chain X [auth B] MOL2 format, chain TB [auth L] MOL2 format, chain SB [auth L] MOL2 format, chain R [auth A] MOL2 format, chain QA [auth F] MOL2 format, chain PA [auth F] MOL2 format, chain OB [auth K] MOL2 format, chain NB [auth K] MOL2 format, chain JC [auth O] MOL2 format, chain IC [auth O] MOL2 format, chain HB [auth I] MOL2 format, chain GB [auth I] MOL2 format, chain FA [auth D] MOL2 format, chain AB [auth H] mmCIF format, chain Y [auth B] mmCIF format, chain XB [auth M] mmCIF format, chain X [auth B] mmCIF format, chain TB [auth L] mmCIF format, chain SB [auth L] mmCIF format, chain R [auth A] mmCIF format, chain QA [auth F] mmCIF format, chain PA [auth F] mmCIF format, chain OB [auth K] mmCIF format, chain NB [auth K] mmCIF format, chain JC [auth O] mmCIF format, chain IC [auth O] mmCIF format, chain HB [auth I] mmCIF format, chain GB [auth I] mmCIF format, chain FA [auth D] mmCIF format, chain AB [auth H]	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		Interactions Focus chain AB [auth H] Focus chain FA [auth D] Focus chain GB [auth I] Focus chain HB [auth I] Focus chain IC [auth O] Focus chain JC [auth O] Focus chain NB [auth K] Focus chain OB [auth K] Focus chain PA [auth F] Focus chain QA [auth F] Focus chain R [auth A] Focus chain SB [auth L] Focus chain TB [auth L] Focus chain X [auth B] Focus chain XB [auth M] Focus chain Y [auth B] Interactions & Density Focus chain AB [auth H] Focus chain FA [auth D] Focus chain GB [auth I] Focus chain HB [auth I] Focus chain IC [auth O] Focus chain JC [auth O] Focus chain NB [auth K] Focus chain OB [auth K] Focus chain PA [auth F] Focus chain QA [auth F] Focus chain R [auth A] Focus chain SB [auth L] Focus chain TB [auth L] Focus chain X [auth B] Focus chain XB [auth M] Focus chain Y [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain YA [auth G] SDF format, chain XA [auth G] SDF format, chain VB [auth L] SDF format, chain T [auth A] SDF format, chain SA [auth F] SDF format, chain RC [auth P] SDF format, chain QC [auth P] SDF format, chain PC [auth P] SDF format, chain OC [auth P] SDF format, chain NC [auth P] SDF format, chain MA [auth D] SDF format, chain LA [auth D] SDF format, chain KA [auth D] SDF format, chain JA [auth D] SDF format, chain GC [auth N] SDF format, chain EB [auth H] SDF format, chain DA [auth C] SDF format, chain BC [auth M] SDF format, chain AC [auth M] MOL2 format, chain YA [auth G] MOL2 format, chain XA [auth G] MOL2 format, chain VB [auth L] MOL2 format, chain T [auth A] MOL2 format, chain SA [auth F] MOL2 format, chain RC [auth P] MOL2 format, chain QC [auth P] MOL2 format, chain PC [auth P] MOL2 format, chain OC [auth P] MOL2 format, chain NC [auth P] MOL2 format, chain MA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain GC [auth N] MOL2 format, chain EB [auth H] MOL2 format, chain DA [auth C] MOL2 format, chain BC [auth M] MOL2 format, chain AC [auth M] mmCIF format, chain YA [auth G] mmCIF format, chain XA [auth G] mmCIF format, chain VB [auth L] mmCIF format, chain T [auth A] mmCIF format, chain SA [auth F] mmCIF format, chain RC [auth P] mmCIF format, chain QC [auth P] mmCIF format, chain PC [auth P] mmCIF format, chain OC [auth P] mmCIF format, chain NC [auth P] mmCIF format, chain MA [auth D] mmCIF format, chain LA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain GC [auth N] mmCIF format, chain EB [auth H] mmCIF format, chain DA [auth C] mmCIF format, chain BC [auth M] mmCIF format, chain AC [auth M]	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		Interactions Focus chain AC [auth M] Focus chain BC [auth M] Focus chain DA [auth C] Focus chain EB [auth H] Focus chain GC [auth N] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NC [auth P] Focus chain OC [auth P] Focus chain PC [auth P] Focus chain QC [auth P] Focus chain RC [auth P] Focus chain SA [auth F] Focus chain T [auth A] Focus chain VB [auth L] Focus chain XA [auth G] Focus chain YA [auth G] Interactions & Density Focus chain AC [auth M] Focus chain BC [auth M] Focus chain DA [auth C] Focus chain EB [auth H] Focus chain GC [auth N] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NC [auth P] Focus chain OC [auth P] Focus chain PC [auth P] Focus chain QC [auth P] Focus chain RC [auth P] Focus chain SA [auth F] Focus chain T [auth A] Focus chain VB [auth L] Focus chain XA [auth G] Focus chain YA [auth G]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain YB [auth M] SDF format, chain VA [auth G] SDF format, chain UB [auth L] SDF format, chain S [auth A] SDF format, chain PB [auth K] SDF format, chain MC [auth P] SDF format, chain LB [auth J] SDF format, chain CB [auth H] SDF format, chain BB [auth H] SDF format, chain BA [auth C] SDF format, chain AA [auth C] MOL2 format, chain YB [auth M] MOL2 format, chain VA [auth G] MOL2 format, chain UB [auth L] MOL2 format, chain S [auth A] MOL2 format, chain PB [auth K] MOL2 format, chain MC [auth P] MOL2 format, chain LB [auth J] MOL2 format, chain CB [auth H] MOL2 format, chain BB [auth H] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain YB [auth M] mmCIF format, chain VA [auth G] mmCIF format, chain UB [auth L] mmCIF format, chain S [auth A] mmCIF format, chain PB [auth K] mmCIF format, chain MC [auth P] mmCIF format, chain LB [auth J] mmCIF format, chain CB [auth H] mmCIF format, chain BB [auth H] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth C]	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		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain BB [auth H] Focus chain CB [auth H] Focus chain LB [auth J] Focus chain MC [auth P] Focus chain PB [auth K] Focus chain S [auth A] Focus chain UB [auth L] Focus chain VA [auth G] Focus chain YB [auth M] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain BB [auth H] Focus chain CB [auth H] Focus chain LB [auth J] Focus chain MC [auth P] Focus chain PB [auth K] Focus chain S [auth A] Focus chain UB [auth L] Focus chain VA [auth G] Focus chain YB [auth M]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free: 0.208 (Depositor), 0.208 (DCC)
R-Value Work: 0.175 (Depositor), 0.175 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.97	α = 90
b = 104.23	β = 102.41
c = 148	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-06-17

Deposition Author(s):

Bonch-Osmolovskaya, E.

Wohlgemuth, R.

Littlechild, J.A.

Montia, D.

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