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P51698 (LINB_SPHPI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 81. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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
OrganismSphingomonas paucimobilis (Pseudomonas paucimobilis)
Taxonomic identifier13689 [NCBI]
Taxonomic lineageBacteriaProteobacteriaAlphaproteobacteriaSphingomonadalesSphingomonadaceaeSphingomonas

Protein attributes

Sequence length296 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence 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.

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 processDetoxification
   Cellular componentPeriplasm
   Molecular functionHydrolase
   Technical term3D-structure
Direct protein sequencing
Gene Ontology (GO)
   Biological_processresponse to toxic substance

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentperiplasmic space

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionhaloalkane dehalogenase activity

Inferred from electronic annotation. Source: UniProtKB-HAMAP

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.1 Ref.4
Chain2 – 296295Haloalkane dehalogenase HAMAP-Rule MF_01231
PRO_0000216778

Sites

Active site1081Nucleophile
Active site1321Proton donor
Active site2721Proton acceptor
Binding site381Halide
Binding site1091Halide

Natural variations

Natural variant811A → T in strain: B90.
Natural variant1121A → V in strain: B90.
Natural variant134 – 1352IA → VT in strain: B90.
Natural variant1381I → L in strain: B90.
Natural variant2471A → H in strain: B90.
Natural variant2531M → I in strain: B90.

Experimental info

Mutagenesis381N → D, E, F or Q: Loss of activity. Ref.7
Mutagenesis1081D → A: Loss of activity. Ref.6
Mutagenesis1081D → N: 58% of wild-type activity. Ref.6
Mutagenesis1091W → L: Loss of activity. Ref.7
Mutagenesis1321E → Q: Loss of activity. Ref.6
Mutagenesis1511F → L, W or Y: Increase in activity. Ref.7
Mutagenesis1691F → L: 31% of wild-type activity. Ref.7
Mutagenesis2441E → Q: 38% of wild-type activity. Ref.6
Mutagenesis2721H → A: Loss of activity. Ref.6

Secondary structure

.......................................................... 296
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P51698 [UniParc].

Last modified January 23, 2007. Version 4.
Checksum: 6EEE011B157DBAE1

FASTA29633,108
        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 

« Hide

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.
PIRA49896.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1CV2X-ray1.58A1-296[»]
1D07X-ray2.00A1-296[»]
1G42X-ray1.80A1-296[»]
1G4HX-ray1.80A1-296[»]
1G5FX-ray1.80A1-296[»]
1IZ7X-ray1.58A2-296[»]
1IZ8X-ray2.00A2-296[»]
1K5PX-ray1.80A2-296[»]
1K63X-ray1.80A2-296[»]
1K6EX-ray1.85A2-296[»]
1MJ5X-ray0.95A1-296[»]
2BFNX-ray1.60A1-296[»]
ProteinModelPortalP51698.
SMRP51698. Positions 2-296.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Enzyme and pathway databases

BioCycMetaCyc:LINBPSEPA-MONOMER.
SABIO-RKP51698.
UniPathwayUPA00689.

Family and domain databases

HAMAPMF_01231. Haloalk_dehal_type2.
InterProIPR000639. Epox_hydrolase-like.
IPR023594. Haloalkane_dehalogenase_2.
[Graphical view]
PRINTSPR00412. EPOXHYDRLASE.
ProtoNetSearch...

Other

EvolutionaryTraceP51698.

Entry information

Entry nameLINB_SPHPI
AccessionPrimary (citable) accession number: P51698
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: January 23, 2007
Last modified: April 16, 2014
This is version 81 of the entry and version 4 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways