P51698 (LINB_PSEPA) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Haloalkane dehalogenase
EC=3.8.1.5

Alternative name(s):
1,3,4,6-tetrachloro-1,4-cyclohexadiene hydrolase
1,4-TCDN chlorohydrolase

Gene names

Name:

linB

Organism

Pseudomonas paucimobilis (Sphingomonas paucimobilis)

Taxonomic identifier

13689 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Alphaproteobacteria › Sphingomonadales › Sphingomonadaceae › Sphingomonas

Protein attributes

Sequence length	296 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 hydrolytic cleavage of carbon-halogen bonds in halogenated aliphatic compounds, leading to the formation of the corresponding primary alcohols, halide ions and protons. Has a broad substrate specificity since not only monochloroalkanes (C3 to C10) but also dichloroalkanes (> C3), bromoalkanes, and chlorinated aliphatic alcohols were good substrates. Shows almost no activity with 1,2-dichloroethane, but very high activity with the brominated analog. Is involved in the degradation of the important environmental pollutant gamma-hexachlorocyclohexane (lindane) as it also catalyzes conversion of 1,3,4,6-tetrachloro-1,4-cyclohexadiene (1,4-TCDN) to 2,5-dichloro-2,5-cyclohexadiene-1,4-diol (2,5-DDOL) via the intermediate 2,4,5-trichloro-2,5-cyclohexadiene-1-ol (2,4,5-DNOL). HAMAP-Rule MF_01231
Catalytic activity	1-haloalkane + H2O = a primary alcohol + halide. HAMAP-Rule MF_01231 1,4-TCDN + 2 H2O = 2,5-DDOL + 2 chloride. HAMAP-Rule MF_01231
Enzyme regulation	Competitively inhibited by the key pollutants 1,2-dichloroethane (1,2-DCE) and 1,2-dichloropropane (1,2-DCP). HAMAP-Rule MF_01231
Pathway	Xenobiotic degradation; gamma-hexachlorocyclohexane degradation. HAMAP-Rule MF_01231
Subunit structure	Monomer.
Subcellular location	Periplasm Ref.4.
Induction	Constitutively expressed. HAMAP-Rule MF_01231
Miscellaneous	Is not N-terminally processed during export, so it may be secreted into the periplasmic space via a hitherto unknown mechanism. HAMAP-Rule MF_01231
Sequence similarities	Belongs to the haloalkane dehalogenase family. Type 2 subfamily.
Biophysicochemical properties	pH dependence: Optimum pH is 8.2. HAMAP-Rule MF_01231

Ontologies

Keywords
Biological process	Detoxification
Cellular component	Periplasm
Molecular function	Hydrolase
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological_process	metabolic process Inferred from electronic annotation. Source: GOC response to toxin Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	periplasmic space Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	haloalkane dehalogenase activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.1 Ref.4

Chain

2 – 296

295

Haloalkane dehalogenase HAMAP-Rule MF_01231

PRO_0000216778

Sites

Active site

108

1

Nucleophile

Active site

132

1

Proton donor

Active site

272

1

Proton acceptor

Binding site

38

1

Halide

Binding site

109

1

Halide

Natural variations

Natural variant

81

1

A → T in strain: B90.

Natural variant

112

1

A → V in strain: B90.

Natural variant

134 – 135

2

IA → VT in strain: B90.

Natural variant

138

1

I → L in strain: B90.

Natural variant

247

1

A → H in strain: B90.

Natural variant

253

1

M → I in strain: B90.

Experimental info

Mutagenesis

38

1

N → D, E, F or Q: Loss of activity. Ref.7

Mutagenesis

108

1

D → A: Loss of activity. Ref.6

Mutagenesis

108

1

D → N: 58% of wild-type activity. Ref.6

Mutagenesis

109

1

W → L: Loss of activity. Ref.7

Mutagenesis

132

1

E → Q: Loss of activity. Ref.6

Mutagenesis

151

1

F → L, W or Y: Increase in activity. Ref.7

Mutagenesis

169

1

F → L: 31% of wild-type activity. Ref.7

Mutagenesis

244

1

E → Q: 38% of wild-type activity. Ref.6

Mutagenesis

272

1

H → A: Loss of activity. Ref.6

Secondary structure

1

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296

Helix Strand Turn

Details...

Beta strand

12 – 16

5

Beta strand

19 – 27

9

Beta strand

29 – 35

7

Helix

42 – 45

4

Turn

46 – 48

3

Helix

49 – 52

4

Beta strand

55 – 61

7

Turn

77 – 80

4

Helix

82 – 95

14

Beta strand

102 – 107

6

Helix

108 – 120

13

Helix

121 – 124

4

Beta strand

125 – 132

8

Helix

140 – 142

3

Helix

145 – 147

3

Helix

148 – 155

8

Helix

159 – 163

5

Turn

164 – 166

3

Helix

168 – 171

4

Helix

173 – 176

4

Beta strand

178 – 180

3

Helix

184 – 191

8

Helix

192 – 194

3

Beta strand

196 – 198

3

Helix

199 – 201

3

Helix

202 – 206

5

Helix

208 – 210

3

Helix

218 – 231

14

Beta strand

238 – 245

8

Beta strand

247 – 250

4

Helix

251 – 257

7

Beta strand

261 – 272

12

Helix

274 – 276

3

Helix

279 – 293

15

Sequences

	Sequence		Length	Mass (Da)
	P51698 [UniParc]. Last modified January 23, 2007. Version 4. Checksum: 6EEE011B157DBAE1	FASTA	296	33,108
	10 20 30 40 50 60 MSLGAKPFGE KKFIEIKGRR MAYIDEGTGD PILFQHGNPT SSYLWRNIMP HCAGLGRLIA 70 80 90 100 110 120 CDLIGMGDSD KLDPSGPERY AYAEHRDYLD ALWEALDLGD RVVLVVHDWG SALGFDWARR 130 140 150 160 170 180 HRERVQGIAY MEAIAMPIEW ADFPEQDRDL FQAFRSQAGE ELVLQDNVFV EQVLPGLILR 190 200 210 220 230 240 PLSEAEMAAY REPFLAAGEA RRPTLSWPRQ IPIAGTPADV VAIARDYAGW LSESPIPKLF 250 260 270 280 290 INAEPGALTT GRMRDFCRTW PNQTEITVAG AHFIQEDSPD EIGAAIAAFV RRLRPA

References

[1]	"Cloning and sequencing of a dehalogenase gene encoding an enzyme with hydrolase activity involved in the degradation of gamma-hexachlorocyclohexane in Pseudomonas paucimobilis." Nagata Y., Nariya T., Ohtomo R., Fukuda M., Yano K., Takagi M. J. Bacteriol. 175:6403-6410(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-16. Strain: UT26.
[2]	Nagata Y., Nariya T., Ohtomo R., Fukuda M., Yano K., Takagi M. Submitted (MAR-1999) to the EMBL/GenBank/DDBJ databases Cited for: SEQUENCE REVISION.
[3]	"Cloning and characterization of lin genes responsible for the degradation of hexachlorocyclohexane isomers by Sphingomonas paucimobilis strain B90." Kumari R., Subudhi S., Suar M., Dhingra G., Raina V., Dogra C., Lal S., van der Meer J.R., Holliger C., Lal R. Appl. Environ. Microbiol. 68:6021-6028(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: B90.
[4]	"Two different types of dehalogenases, LinA and LinB, involved in gamma-hexachlorocyclohexane degradation in Sphingomonas paucimobilis UT26 are localized in the periplasmic space without molecular processing." Nagata Y., Futamura A., Miyauchi K., Takagi M. J. Bacteriol. 181:5409-5413(1999) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-10, SUBCELLULAR LOCATION.
[5]	"Purification and characterization of a haloalkane dehalogenase of a new substrate class from a gamma-hexachlorocyclohexane-degrading bacterium, Sphingomonas paucimobilis UT26." Nagata Y., Miyauchi K., Damborsky J., Manova K., Ansorgova A., Takagi M. Appl. Environ. Microbiol. 63:3707-3710(1997) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION. Strain: UT26.
[6]	"Identification of the catalytic triad in the haloalkane dehalogenase from Sphingomonas paucimobilis UT26." Hynkova K., Nagata Y., Takagi M., Damborsky J. FEBS Lett. 446:177-181(1999) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF ASP-108; GLU-132; GLU-244 AND HIS-272. Strain: UT26.
[7]	"Halide-stabilizing residues of haloalkane dehalogenases studied by quantum mechanic calculations and site-directed mutagenesis." Bohac M., Nagata Y., Prokop Z., Prokop M., Monincova M., Tsuda M., Koca J., Damborsky J. Biochemistry 41:14272-14280(2002) [PubMed] [Europe PMC] [Abstract] Cited for: QUANTUM MECHANIC STUDIES, MUTAGENESIS OF ASN-38; TRP-109; PHE-151 AND PHE-169.
[8]	"Crystallization and preliminary X-ray diffraction analysis of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26." Smatanova I.K., Nagata Y., Svensson L.A., Takagi M., Marek J. Acta Crystallogr. D 55:1231-1233(1999) [PubMed] [Europe PMC] [Abstract] Cited for: CRYSTALLIZATION. Strain: UT26.
[9]	"Crystal structure of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26." Marek J., Vevodova J., Smatanova I.K., Nagata Y., Svensson L.A., Newman J., Takagi M., Damborsky J. Biochemistry 39:14082-14086(2000) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.58 ANGSTROMS) OF NATIVE PROTEIN AND COMPLEX WITH 1,3-PROPANEDIOL. Strain: UT26.
[10]	"Exploring the structure and activity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26: evidence for product- and water-mediated inhibition." Oakley A.J., Prokop Z., Bohac M., Kmunicek J., Jedlicka T., Monincova M., Kuta-Smatanova I., Nagata Y., Damborsky J., Wilce M.C.J. Biochemistry 41:4847-4855(2002) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF COMPLEXES WITH 1,2-DICHLOROETHANE; 1,2-DICHLOROPROPANE AND BUTAN-1-OL. Strain: UT26.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

D14594 Genomic DNA. Translation: BAA03443.2.
AY150581 Genomic DNA. Translation: AAN64241.1.

PIR

A49896.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1CV2	X-ray	1.58	A	1-296	[»]
1D07	X-ray	2.00	A	1-296	[»]
1G42	X-ray	1.80	A	1-296	[»]
1G4H	X-ray	1.80	A	1-296	[»]
1G5F	X-ray	1.80	A	1-296	[»]
1IZ7	X-ray	1.58	A	2-296	[»]
1IZ8	X-ray	2.00	A	2-296	[»]
1K5P	X-ray	1.80	A	2-296	[»]
1K63	X-ray	1.80	A	2-296	[»]
1K6E	X-ray	1.85	A	2-296	[»]
1MJ5	X-ray	0.95	A	1-296	[»]
2BFN	X-ray	1.60	A	1-296	[»]

ProteinModelPortal

P51698.

SMR

P51698. Positions 2-296.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Enzyme and pathway databases

BioCyc

MetaCyc:LINBPSEPA-MONOMER.

SABIO-RK

P51698.

UniPathway

UPA00689.

Family and domain databases

HAMAP

MF_01231. Haloalk_dehal_type2.

InterPro

IPR000639. Epox_hydrolase-like.
IPR023594. Haloalkane_dehalogenase_2.
[Graphical view]

PRINTS

PR00412. EPOXHYDRLASE.

ProtoNet

Search...

Other

EvolutionaryTrace

P51698.

Entry information

Entry name

LINB_PSEPA

Accession

Primary (citable) accession number: P51698

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1996
Last sequence update:	January 23, 2007
Last modified:	April 3, 2013
This is version 76 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program