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Protein

Sulfite reductase, dissimilatory-type subunit beta

Gene

dsvB

Organism
Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the reduction of sulfite to sulfide. This is the terminal oxidation reaction in sulfate respiration, a process catalyzed by the sulfate-reducing bacteria.2 Publications

Catalytic activityi

Hydrogen sulfide + a [DsrC protein]-disulfide + 2 acceptor + 3 H2O = sulfite + a [DsrC protein]-dithiol + 2 reduced acceptor + 2 H+.2 Publications
A [DsrC protein]-S-sulfanyl-L-cysteine + 3 acceptor + 3 H2O = sulfite + a [DsrC protein]-disulfide + 3 reduced acceptor + 2 H+.2 Publications

Cofactori

Protein has several cofactor binding sites:
  • [4Fe-4S] cluster1 PublicationNote: Binds 2 [4Fe-4S] clusters per subunit.1 Publication
  • siroheme1 PublicationNote: Binds 1 siroheme per subunit.1 Publication

Kineticsi

kcat is 0.31 (sec-1) for sulfite. kcat is 0.038 (sec-1) for nitrite.1 Publication

  1. KM=0.06 mM for sulfite1 Publication
  2. KM=0.028 mM for nitrite1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi151 – 1511Iron-sulfur (4Fe-4S) 1Combined sources1 Publication
    Metal bindingi188 – 1881Iron-sulfur (4Fe-4S) 1Combined sources1 Publication
    Metal bindingi189 – 1891Iron-sulfur (4Fe-4S) 1Combined sources1 Publication
    Metal bindingi193 – 1931Iron (siroheme axial ligand)1 Publication
    Metal bindingi193 – 1931Iron-sulfur (4Fe-4S) 1Combined sources1 Publication
    Metal bindingi231 – 2311Iron-sulfur (4Fe-4S) 2Combined sources1 Publication
    Metal bindingi258 – 2581Iron-sulfur (4Fe-4S) 2Combined sources1 Publication
    Metal bindingi261 – 2611Iron-sulfur (4Fe-4S) 2Combined sources1 Publication
    Metal bindingi264 – 2641Iron-sulfur (4Fe-4S) 2Combined sources1 Publication

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    4Fe-4S, Iron, Iron-sulfur, Metal-binding

    Enzyme and pathway databases

    BioCyciDVUL882:GJIL-423-MONOMER.
    MetaCyc:MONOMER-12512.
    BRENDAi1.8.99.3. 1914.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Sulfite reductase, dissimilatory-type subunit beta (EC:1.8.99.52 Publications)
    Alternative name(s):
    Desulfoviridin subunit beta1 Publication
    Dissimilatory sulfite reductase subunit beta1 Publication
    Short name:
    dSiR beta1 Publication
    Hydrogensulfite reductase subunit beta
    Gene namesi
    Name:dsvB
    Synonyms:dsrB1 Publication
    Ordered Locus Names:DVU_0403
    OrganismiDesulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)
    Taxonomic identifieri882 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio
    Proteomesi
    • UP000002194 Componenti: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methionineiRemoved1 Publication
    Chaini2 – 381380Sulfite reductase, dissimilatory-type subunit betaPRO_0000080032Add
    BLAST

    Proteomic databases

    PaxDbiP45575.

    Interactioni

    Subunit structurei

    Heterohexamer of two alpha, two beta and two gamma subunits.2 Publications

    Protein-protein interaction databases

    STRINGi882.DVU0403.

    Structurei

    Secondary structure

    1
    381
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Turni13 – 164Combined sources
    Turni26 – 294Combined sources
    Helixi32 – 376Combined sources
    Beta strandi41 – 488Combined sources
    Beta strandi51 – 566Combined sources
    Beta strandi61 – 677Combined sources
    Beta strandi71 – 744Combined sources
    Helixi75 – 8814Combined sources
    Beta strandi92 – 954Combined sources
    Beta strandi101 – 1077Combined sources
    Helixi108 – 12013Combined sources
    Beta strandi128 – 1303Combined sources
    Beta strandi136 – 1394Combined sources
    Helixi147 – 1493Combined sources
    Helixi159 – 17315Combined sources
    Beta strandi178 – 1803Combined sources
    Beta strandi184 – 1896Combined sources
    Helixi196 – 1983Combined sources
    Beta strandi199 – 2068Combined sources
    Helixi215 – 2217Combined sources
    Helixi224 – 2296Combined sources
    Beta strandi236 – 2438Combined sources
    Beta strandi246 – 2538Combined sources
    Helixi255 – 2573Combined sources
    Helixi263 – 2675Combined sources
    Turni276 – 2783Combined sources
    Beta strandi280 – 2856Combined sources
    Beta strandi292 – 2943Combined sources
    Beta strandi300 – 3078Combined sources
    Turni310 – 3123Combined sources
    Helixi314 – 33017Combined sources
    Helixi337 – 3448Combined sources
    Helixi346 – 3538Combined sources
    Helixi359 – 3613Combined sources
    Helixi367 – 3726Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2V4JX-ray2.10B/E1-381[»]
    ProteinModelPortaliP45575.
    SMRiP45575. Positions 15-381.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP45575.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini249 – 276284Fe-4S ferredoxin-typePROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Contains 1 4Fe-4S ferredoxin-type domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiENOG4105PJW. Bacteria.
    COG2221. LUCA.
    KOiK11181.
    OMAiWLHCDIP.
    OrthoDBiEOG6PKF8Z.

    Family and domain databases

    InterProiIPR017896. 4Fe4S_Fe-S-bd.
    IPR017900. 4Fe4S_Fe_S_CS.
    IPR011808. DsrB.
    IPR005117. NiRdtase/SiRdtase_haem-b_fer.
    IPR006067. NO2/SO3_Rdtase_4Fe4S_dom.
    [Graphical view]
    PfamiPF01077. NIR_SIR. 1 hit.
    PF03460. NIR_SIR_ferr. 1 hit.
    [Graphical view]
    SUPFAMiSSF55124. SSF55124. 1 hit.
    TIGRFAMsiTIGR02066. dsrB. 1 hit.
    PROSITEiPS00198. 4FE4S_FER_1. 1 hit.
    PS51379. 4FE4S_FER_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P45575-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MAFISSGYNP EKPMANRITD IGPRKFDEFF PPVIAKNFGS WLYHEILEPG
    60 70 80 90 100
    VLMHVAESGD KVYTVRVGAA RLMSITHIRE MCDIADKYCG GHLRFTTRNN
    110 120 130 140 150
    VEFMVADEAS LKALKEDLAS RKFDGGSLKF PIGGTGAGVS NIVHTQGWVH
    160 170 180 190 200
    CHTPATDASG PVKAIMDEVF EDFQSMRLPA PVRISLACCI NMCGAVHCSD
    210 220 230 240 250
    IGVVGIHRKP PMIDHEWTDQ LCEIPLAVAS CPTAAVRPTK LEIGDKKVNT
    260 270 280 290 300
    IAIKNERCMY CGNCYTMCPA LPISDGEGDG VVIMVGGKVS NRISMPKFSK
    310 320 330 340 350
    VVVAYIPNEP PRWPSLTKTI KHIIEVYSAN AYKYERLGEW AERIGWERFF
    360 370 380
    SLTGLEFSHH LIDDFRDPAY YTWRQSTQFK F
    Length:381
    Mass (Da):42,519
    Last modified:January 23, 2007 - v3
    Checksum:i678A04F716050D63
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U16723 Genomic DNA. Translation: AAA70108.1.
    AE017285 Genomic DNA. Translation: AAS94886.1.
    PIRiS21238.
    RefSeqiWP_010937710.1. NC_002937.3.
    YP_009627.1. NC_002937.3.

    Genome annotation databases

    EnsemblBacteriaiAAS94886; AAS94886; DVU_0403.
    GeneIDi2796153.
    KEGGidvu:DVU0403.
    PATRICi32060774. VBIDesVul119526_0380.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U16723 Genomic DNA. Translation: AAA70108.1.
    AE017285 Genomic DNA. Translation: AAS94886.1.
    PIRiS21238.
    RefSeqiWP_010937710.1. NC_002937.3.
    YP_009627.1. NC_002937.3.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2V4JX-ray2.10B/E1-381[»]
    ProteinModelPortaliP45575.
    SMRiP45575. Positions 15-381.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi882.DVU0403.

    Proteomic databases

    PaxDbiP45575.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAS94886; AAS94886; DVU_0403.
    GeneIDi2796153.
    KEGGidvu:DVU0403.
    PATRICi32060774. VBIDesVul119526_0380.

    Phylogenomic databases

    eggNOGiENOG4105PJW. Bacteria.
    COG2221. LUCA.
    KOiK11181.
    OMAiWLHCDIP.
    OrthoDBiEOG6PKF8Z.

    Enzyme and pathway databases

    BioCyciDVUL882:GJIL-423-MONOMER.
    MetaCyc:MONOMER-12512.
    BRENDAi1.8.99.3. 1914.

    Miscellaneous databases

    EvolutionaryTraceiP45575.

    Family and domain databases

    InterProiIPR017896. 4Fe4S_Fe-S-bd.
    IPR017900. 4Fe4S_Fe_S_CS.
    IPR011808. DsrB.
    IPR005117. NiRdtase/SiRdtase_haem-b_fer.
    IPR006067. NO2/SO3_Rdtase_4Fe4S_dom.
    [Graphical view]
    PfamiPF01077. NIR_SIR. 1 hit.
    PF03460. NIR_SIR_ferr. 1 hit.
    [Graphical view]
    SUPFAMiSSF55124. SSF55124. 1 hit.
    TIGRFAMsiTIGR02066. dsrB. 1 hit.
    PROSITEiPS00198. 4FE4S_FER_1. 1 hit.
    PS51379. 4FE4S_FER_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Conservation of the genes for dissimilatory sulfite reductase from Desulfovibrio vulgaris and Archaeoglobus fulgidus allows their detection by PCR."
      Karkhoff-Schweizer R.R., Huber D.P.W., Voordouw G.
      Appl. Environ. Microbiol. 61:290-296(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: Hildenborough / ATCC 29579 / NCIMB 8303.
    3. "The third subunit of desulfoviridin-type dissimilatory sulfite reductases."
      Pierik A.J., Duyvis M.G., van Helvoort J.M.L.M., Wolbert R.B.G., Hagen W.R.
      Eur. J. Biochem. 205:111-115(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-16, SUBUNIT.
    4. "Isolation of assimilatroy- and dissimilatory-type sulfite reductases from Desulfovibrio vulgaris."
      Lee J.-P., LeGall J., Peck H.D. Jr.
      J. Bacteriol. 115:529-542(1973) [PubMed] [Europe PMC] [Abstract]
      Cited for: CATALYTIC ACTIVITY.
    5. "Desulfoviridin, a multimeric-dissimilatory sulfite reductase from Desulfovibrio vulgaris (Hildenborough). Purification, characterization, kinetics and EPR studies."
      Wolfe B.M., Lui S.M., Cowan J.A.
      Eur. J. Biochem. 223:79-89(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, EPR SPECTROSCOPY, BIOPHYSICOCHEMICAL PROPERTIES.
    6. "The crystal structure of Desulfovibrio vulgaris dissimilatory sulfite reductase bound to DsrC provides novel insights into the mechanism of sulfate respiration."
      Oliveira T.F., Vonrhein C., Matias P.M., Venceslau S.S., Pereira I.A.C., Archer M.
      J. Biol. Chem. 283:34141-34149(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) IN COMPLEX WITH DSVA; DSVC; IRON-SULFUR (4FE-4S) AND SIROHEME, SUBUNIT, COFACTOR, REACTION MECHANISM.

    Entry informationi

    Entry nameiDSVB_DESVH
    AccessioniPrimary (citable) accession number: P45575
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1995
    Last sequence update: January 23, 2007
    Last modified: December 9, 2015
    This is version 106 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

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

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.