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P51698

- LINB_SPHPI

UniProt

P51698 - LINB_SPHPI

Protein

Haloalkane dehalogenase

Gene

linB

Organism
Sphingomonas paucimobilis (Pseudomonas paucimobilis)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 83 (01 Oct 2014)
      Sequence version 4 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    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).

    Catalytic activityi

    1-haloalkane + H2O = a primary alcohol + halide.
    1,4-TCDN + 2 H2O = 2,5-DDOL + 2 chloride.

    Enzyme regulationi

    Competitively inhibited by the key pollutants 1,2-dichloroethane (1,2-DCE) and 1,2-dichloropropane (1,2-DCP).

    pH dependencei

    Optimum pH is 8.2.

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei38 – 381Halide
    Active sitei108 – 1081Nucleophile
    Binding sitei109 – 1091Halide
    Active sitei132 – 1321Proton donor
    Active sitei272 – 2721Proton acceptor

    GO - Molecular functioni

    1. haloalkane dehalogenase activity Source: UniProtKB-HAMAP

    GO - Biological processi

    1. response to toxic substance Source: UniProtKB-KW

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Detoxification

    Enzyme and pathway databases

    BioCyciMetaCyc:LINBPSEPA-MONOMER.
    SABIO-RKP51698.
    UniPathwayiUPA00689.

    Names & Taxonomyi

    Protein namesi
    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 namesi
    Name:linB
    OrganismiSphingomonas paucimobilis (Pseudomonas paucimobilis)
    Taxonomic identifieri13689 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaSphingomonadalesSphingomonadaceaeSphingomonas

    Subcellular locationi

    Periplasm 1 Publication

    GO - Cellular componenti

    1. periplasmic space Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Periplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi38 – 381N → D, E, F or Q: Loss of activity. 1 Publication
    Mutagenesisi108 – 1081D → A: Loss of activity. 1 Publication
    Mutagenesisi108 – 1081D → N: 58% of wild-type activity. 1 Publication
    Mutagenesisi109 – 1091W → L: Loss of activity. 1 Publication
    Mutagenesisi132 – 1321E → Q: Loss of activity. 1 Publication
    Mutagenesisi151 – 1511F → L, W or Y: Increase in activity. 1 Publication
    Mutagenesisi169 – 1691F → L: 31% of wild-type activity. 1 Publication
    Mutagenesisi244 – 2441E → Q: 38% of wild-type activity. 1 Publication
    Mutagenesisi272 – 2721H → A: Loss of activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed2 Publications
    Chaini2 – 296295Haloalkane dehalogenasePRO_0000216778Add
    BLAST

    Expressioni

    Inductioni

    Constitutively expressed.

    Interactioni

    Subunit structurei

    Monomer.

    Structurei

    Secondary structure

    1
    296
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi12 – 165
    Beta strandi19 – 279
    Beta strandi29 – 357
    Helixi42 – 454
    Turni46 – 483
    Helixi49 – 524
    Beta strandi55 – 617
    Turni77 – 804
    Helixi82 – 9514
    Beta strandi102 – 1076
    Helixi108 – 12013
    Helixi121 – 1244
    Beta strandi125 – 1328
    Helixi140 – 1423
    Helixi145 – 1473
    Helixi148 – 1558
    Helixi159 – 1635
    Turni164 – 1663
    Helixi168 – 1714
    Helixi173 – 1764
    Beta strandi178 – 1803
    Helixi184 – 1918
    Helixi192 – 1943
    Beta strandi196 – 1983
    Helixi199 – 2013
    Helixi202 – 2065
    Helixi208 – 2103
    Helixi218 – 23114
    Beta strandi238 – 2458
    Beta strandi247 – 2504
    Helixi251 – 2577
    Beta strandi261 – 27212
    Helixi274 – 2763
    Helixi279 – 29315

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    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[»]
    ProteinModelPortaliP51698.
    SMRiP51698. Positions 2-296.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP51698.

    Family & Domainsi

    Sequence similaritiesi

    Family and domain databases

    Gene3Di3.40.50.1820. 1 hit.
    HAMAPiMF_01231. Haloalk_dehal_type2.
    InterProiIPR029058. AB_hydrolase.
    IPR000639. Epox_hydrolase-like.
    IPR023594. Haloalkane_dehalogenase_2.
    [Graphical view]
    PRINTSiPR00412. EPOXHYDRLASE.
    SUPFAMiSSF53474. SSF53474. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P51698-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSLGAKPFGE KKFIEIKGRR MAYIDEGTGD PILFQHGNPT SSYLWRNIMP    50
    HCAGLGRLIA CDLIGMGDSD KLDPSGPERY AYAEHRDYLD ALWEALDLGD 100
    RVVLVVHDWG SALGFDWARR HRERVQGIAY MEAIAMPIEW ADFPEQDRDL 150
    FQAFRSQAGE ELVLQDNVFV EQVLPGLILR PLSEAEMAAY REPFLAAGEA 200
    RRPTLSWPRQ IPIAGTPADV VAIARDYAGW LSESPIPKLF INAEPGALTT 250
    GRMRDFCRTW PNQTEITVAG AHFIQEDSPD EIGAAIAAFV RRLRPA 296
    Length:296
    Mass (Da):33,108
    Last modified:January 23, 2007 - v4
    Checksum:i6EEE011B157DBAE1
    GO

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti81 – 811A → T in strain: B90.
    Natural varianti112 – 1121A → V in strain: B90.
    Natural varianti134 – 1352IA → VT in strain: B90.
    Natural varianti138 – 1381I → L in strain: B90.
    Natural varianti247 – 2471A → H in strain: B90.
    Natural varianti253 – 2531M → I in strain: B90.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D14594 Genomic DNA. Translation: BAA03443.2.
    AY150581 Genomic DNA. Translation: AAN64241.1.
    PIRiA49896.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D14594 Genomic DNA. Translation: BAA03443.2 .
    AY150581 Genomic DNA. Translation: AAN64241.1 .
    PIRi A49896.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    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 [» ]
    ProteinModelPortali P51698.
    SMRi P51698. Positions 2-296.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Enzyme and pathway databases

    UniPathwayi UPA00689 .
    BioCyci MetaCyc:LINBPSEPA-MONOMER.
    SABIO-RK P51698.

    Miscellaneous databases

    EvolutionaryTracei P51698.

    Family and domain databases

    Gene3Di 3.40.50.1820. 1 hit.
    HAMAPi MF_01231. Haloalk_dehal_type2.
    InterProi IPR029058. AB_hydrolase.
    IPR000639. Epox_hydrolase-like.
    IPR023594. Haloalkane_dehalogenase_2.
    [Graphical view ]
    PRINTSi PR00412. EPOXHYDRLASE.
    SUPFAMi SSF53474. SSF53474. 1 hit.
    ProtoNeti Search...

    Publicationsi

    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.

    Entry informationi

    Entry nameiLINB_SPHPI
    AccessioniPrimary (citable) accession number: P51698
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1996
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 83 of the entry and version 4 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Is not N-terminally processed during export, so it may be secreted into the periplasmic space via a hitherto unknown mechanism.

    Keywords - Technical termi

    3D-structure, Direct protein sequencing

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3