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P51698

- LINB_SPHPI

UniProt

P51698 - LINB_SPHPI

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Protein

Haloalkane dehalogenase

Gene
linB
Organism
Sphingomonas paucimobilis (Pseudomonas paucimobilis)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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).UniRule annotation

Catalytic activityi

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

Enzyme regulationi

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

pH dependencei

Optimum pH is 8.2.UniRule annotation

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
Complete GO annotation...

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
Complete GO annotation...

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 dehalogenaseUniRule annotationPRO_0000216778Add
BLAST

Expressioni

Inductioni

Constitutively expressed.UniRule annotation

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.

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: June 11, 2014
This is version 82 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

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