Q9ZAG3 (LIMA_RHOER) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Limonene-1,2-epoxide hydrolase
EC=3.3.2.8

Gene names

Name:

limA

Organism

Rhodococcus erythropolis (Arthrobacter picolinophilus)

Taxonomic identifier

1833 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Actinobacteria › Actinobacteria › Actinobacteridae › Actinomycetales › Corynebacterineae › Nocardiaceae › Rhodococcus

Protein attributes

Sequence length	149 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the conversion of limonene-1,2-epoxide to limonene-1,2-diol. Can use both the (-) and (+) isomers of limonene-1,2-epoxide as substrates and also has some activity with 1-methylcyclohexene oxide, cyclohexene oxide and indene oxide as substrates.
Catalytic activity	1,2-epoxymenth-8-ene + H2O = menth-8-ene-1,2-diol. Ref.3
Pathway	Terpene metabolism; (4R)-limonene degradation; (1S,4R)-1-hydroxylimonen-2-one from (4R)-limonene: step 2/3.
Subunit structure	Monomer. Ref.3
Induction	By growth on monoterpenes.
Sequence similarities	Belongs to the limonene-1,2-epoxide hydrolase family.
Biophysicochemical properties	pH dependence: Optimum pH is 7. Ref.3 Temperature dependence: Optimum temperature is 50 degrees Celsius.

Ontologies

Keywords
Molecular function	Hydrolase
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Molecular_function	limonene-1,2-epoxide hydrolase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.3

Chain

2 – 149

148

Limonene-1,2-epoxide hydrolase

PRO_0000084422

Sites

Active site

101

1

Proton donor Probable

Active site

132

1

Proton acceptor Probable

Experimental info

Mutagenesis

53

1

Y → F: 15% of wild-type catalytic efficiency. Ref.4

Mutagenesis

55

1

N → A: Almost no activity. Ref.4

Mutagenesis

55

1

N → D: No activity. Ref.4

Mutagenesis

99

1

R → A, H, K or Q: Impaired protein folding and no activity. Ref.4

Mutagenesis

101

1

D → A or N: No activity. Ref.4

Mutagenesis

132

1

D → A or N: No activity. Ref.4

Secondary structure

1

.

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.

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.

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149

Helix Strand Turn

Details...

Turn

15 – 18

4

Helix

23 – 34

12

Helix

35 – 37

3

Helix

40 – 44

5

Beta strand

52 – 55

4

Beta strand

61 – 63

3

Helix

64 – 77

14

Beta strand

78 – 91

14

Beta strand

94 – 105

12

Turn

106 – 108

3

Beta strand

111 – 123

13

Beta strand

126 – 133

8

Helix

136 – 143

8

Sequences

	Sequence		Length	Mass (Da)
	Q9ZAG3 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 1A8602D20793A1B9	FASTA	149	16,521
	10 20 30 40 50 60 MTSKIEQPRW ASKDSAAGAA STPDEKIVLE FMDALTSNDA AKLIEYFAED TMYQNMPLPP 70 80 90 100 110 120 AYGRDAVEQT LAGLFTVMSI DAVETFHIGS SNGLVYTERV DVLRALPTGK SYNLSILGVF 130 140 QLTEGKITGW RDYFDLREFE EAVDLPLRG

References

[1]	"The Rhodococcus erythropolis DCL14 limonene-1,2-epoxide hydrolase gene encodes an enzyme belonging to a novel class of epoxide hydrolases." Barbirato F., Verdoes J.C., de Bont J.A.M., van der Werf M.J. FEBS Lett. 438:293-296(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: DCL 14.
[2]	"Genetic analysis of the lim operon of Rhodococcus erythropolis DCL14." Van der Vlugt-Bergmans C.J.B., van der Werf M.J. Submitted (JUL-2000) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: DCL 14.
[3]	"Limonene-1,2-epoxide hydrolase from Rhodococcus erythropolis DCL14 belongs to a novel class of epoxide hydrolases." van der Werf M.J., Overkamp K.M., de Bont J.A.M. J. Bacteriol. 180:5052-5057(1998) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-51, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
[4]	"Structure of Rhodococcus erythropolis limonene-1,2-epoxide hydrolase reveals a novel active site." Arand M., Hallberg B.M., Zou J., Bergfors T., Oesch F., van der Werf M.J., de Bont J.A., Jones T.A., Mowbray S.L. EMBO J. 22:2583-2592(2003) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.2 ANGSTROMS) IN COMPLEX WITH INHIBITOR, MUTAGENESIS OF TYR-53; ASN-55; ARG-99; ASP-101 AND ASP-132, PUTATIVE REACTION MECHANISM.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

Y18005 Genomic DNA. Translation: CAA77012.1.
AJ272366 Genomic DNA. Translation: CAC20854.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1NU3	X-ray	1.75	A/B	3-149	[»]
1NWW	X-ray	1.20	A/B	1-149	[»]

ProteinModelPortal

Q9ZAG3.

SMR

Q9ZAG3. Positions 3-149.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Enzyme and pathway databases

BioCyc

MetaCyc:MONOMER-13975.

BRENDA

3.3.2.8. 5389.

UniPathway

UPA00987; UER00865.

Family and domain databases

InterPro

IPR013100. LEH.
[Graphical view]

Pfam

PF07858. LEH. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q9ZAG3.

Entry information

Entry name

LIMA_RHOER

Accession

Primary (citable) accession number: Q9ZAG3

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 2002
Last sequence update:	January 23, 2007
Last modified:	April 3, 2013
This is version 56 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program