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P13063

- PHSS_DESBA

UniProt

P13063 - PHSS_DESBA

Protein

Periplasmic [NiFeSe] hydrogenase small subunit

Gene
N/A
Organism
Desulfomicrobium baculatum (Desulfovibrio baculatus)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 101 (01 Oct 2014)
      Sequence version 1 (01 Jan 1990)
      Previous versions | rss
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    Functioni

    Catalytic activityi

    H2 + A = AH2.

    Cofactori

    Binds 3 4Fe-4S clusters. Cluster 1 is referred to as proximal, cluster 2 as distal, cluster 3 as medial.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi50 – 501Iron-sulfur 1 (4Fe-4S)
    Metal bindingi53 – 531Iron-sulfur 1 (4Fe-4S)
    Metal bindingi158 – 1581Iron-sulfur 1 (4Fe-4S)
    Metal bindingi196 – 1961Iron-sulfur 1 (4Fe-4S)
    Metal bindingi240 – 2401Iron-sulfur 2 (4Fe-4S); via pros nitrogen
    Metal bindingi243 – 2431Iron-sulfur 2 (4Fe-4S)
    Metal bindingi263 – 2631Iron-sulfur 2 (4Fe-4S)
    Metal bindingi269 – 2691Iron-sulfur 2 (4Fe-4S)
    Metal bindingi278 – 2781Iron-sulfur 3 (4Fe-4S)
    Metal bindingi290 – 2901Iron-sulfur 3 (4Fe-4S)
    Metal bindingi296 – 2961Iron-sulfur 3 (4Fe-4S)
    Metal bindingi299 – 2991Iron-sulfur 3 (4Fe-4S)

    GO - Molecular functioni

    1. 4 iron, 4 sulfur cluster binding Source: UniProtKB-KW
    2. ferredoxin hydrogenase activity Source: InterPro
    3. hydrogenase (acceptor) activity Source: UniProtKB-EC
    4. metal ion binding Source: UniProtKB-KW

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

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

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Periplasmic [NiFeSe] hydrogenase small subunit (EC:1.12.99.6)
    Alternative name(s):
    NiFeSe hydrogenlyase small chain
    OrganismiDesulfomicrobium baculatum (Desulfovibrio baculatus)
    Taxonomic identifieri899 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfomicrobiaceaeDesulfomicrobium

    Subcellular locationi

    GO - Cellular componenti

    1. ferredoxin hydrogenase complex Source: InterPro
    2. periplasmic space Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Periplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 3232Tat-type signal1 PublicationPROSITE-ProRule annotationAdd
    BLAST
    Chaini33 – 315283Periplasmic [NiFeSe] hydrogenase small subunitPRO_0000013420Add
    BLAST

    Post-translational modificationi

    Predicted to be exported by the Tat system. The position of the signal peptide cleavage has been experimentally proven.

    Interactioni

    Subunit structurei

    Heterodimer of a large and a small subunit.

    Protein-protein interaction databases

    DIPiDIP-6126N.
    MINTiMINT-96877.

    Structurei

    Secondary structure

    1
    315
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi40 – 489
    Helixi52 – 587
    Turni61 – 644
    Helixi65 – 717
    Beta strandi73 – 775
    Turni79 – 813
    Helixi86 – 9914
    Turni100 – 1023
    Beta strandi103 – 11311
    Helixi115 – 1184
    Beta strandi121 – 1277
    Beta strandi129 – 1313
    Beta strandi133 – 1375
    Helixi138 – 1458
    Helixi146 – 1483
    Beta strandi149 – 1568
    Helixi157 – 1615
    Helixi164 – 1663
    Helixi177 – 1848
    Beta strandi190 – 1934
    Beta strandi195 – 1973
    Helixi200 – 21516
    Turni217 – 2193
    Helixi232 – 2354
    Beta strandi236 – 2383
    Helixi240 – 2423
    Helixi246 – 2505
    Beta strandi260 – 2645
    Helixi265 – 2673
    Helixi271 – 2733
    Helixi278 – 2814
    Turni284 – 2874
    Helixi290 – 2934
    Turni302 – 3054
    Helixi306 – 3083

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1CC1X-ray2.15S33-315[»]
    4KL8X-ray1.52S/T33-315[»]
    4KN9X-ray1.40S/T33-315[»]
    4KO1X-ray1.55S/T33-315[»]
    4KO2X-ray1.60S/T33-315[»]
    4KO3X-ray1.70S/T33-315[»]
    4KO4X-ray2.00S/T33-315[»]
    ProteinModelPortaliP13063.
    SMRiP13063. Positions 38-315.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP13063.

    Family & Domainsi

    Sequence similaritiesi

    Keywords - Domaini

    Signal

    Family and domain databases

    Gene3Di3.40.50.700. 1 hit.
    4.10.480.10. 1 hit.
    InterProiIPR027394. Cytochrome-c3_hydrogenase_C.
    IPR006137. NADH_UbQ_OxRdtase-like_20kDa.
    IPR001821. NiFe_hydrogenase_ssu.
    IPR006311. TAT_signal.
    IPR019546. TAT_signal_bac_arc.
    [Graphical view]
    PfamiPF14720. NiFe_hyd_SSU_C. 1 hit.
    PF01058. Oxidored_q6. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000310. NiFe_hyd_ssu. 1 hit.
    PRINTSiPR00614. NIHGNASESMLL.
    TIGRFAMsiTIGR00391. hydA. 1 hit.
    TIGR01409. TAT_signal_seq. 1 hit.
    PROSITEiPS51318. TAT. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P13063-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSLSRREFVK LCSAGVAGLG ISQIYHPGIV HAMTEGAKKA PVIWVQGQGC    50
    TGCSVSLLNA VHPRIKEILL DVISLEFHPT VMASEGEMAL AHMYEIAEKF 100
    NGNFFLLVEG AIPTAKEGRY CIVGETLDAK GHHHEVTMME LIRDLAPKSL 150
    ATVAVGTCSA YGGIPAAEGN VTGSKSVRDF FADEKIEKLL VNVPGCPPHP 200
    DWMVGTLVAA WSHVLNPTEH PLPELDDDGR PLLFFGDNIH ENCPYLDKYD 250
    NSEFAETFTK PGCKAELGCK GPSTYADCAK RRWNNGINWC VENAVCIGCV 300
    EPDFPDGKSP FYVAE 315
    Length:315
    Mass (Da):34,221
    Last modified:January 1, 1990 - v1
    Checksum:iA3C592F12B95ED83
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M18271 Genomic DNA. Translation: AAA23376.1.
    PIRiA28380. HQDVSB.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M18271 Genomic DNA. Translation: AAA23376.1 .
    PIRi A28380. HQDVSB.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1CC1 X-ray 2.15 S 33-315 [» ]
    4KL8 X-ray 1.52 S/T 33-315 [» ]
    4KN9 X-ray 1.40 S/T 33-315 [» ]
    4KO1 X-ray 1.55 S/T 33-315 [» ]
    4KO2 X-ray 1.60 S/T 33-315 [» ]
    4KO3 X-ray 1.70 S/T 33-315 [» ]
    4KO4 X-ray 2.00 S/T 33-315 [» ]
    ProteinModelPortali P13063.
    SMRi P13063. Positions 38-315.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-6126N.
    MINTi MINT-96877.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Miscellaneous databases

    EvolutionaryTracei P13063.

    Family and domain databases

    Gene3Di 3.40.50.700. 1 hit.
    4.10.480.10. 1 hit.
    InterProi IPR027394. Cytochrome-c3_hydrogenase_C.
    IPR006137. NADH_UbQ_OxRdtase-like_20kDa.
    IPR001821. NiFe_hydrogenase_ssu.
    IPR006311. TAT_signal.
    IPR019546. TAT_signal_bac_arc.
    [Graphical view ]
    Pfami PF14720. NiFe_hyd_SSU_C. 1 hit.
    PF01058. Oxidored_q6. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF000310. NiFe_hyd_ssu. 1 hit.
    PRINTSi PR00614. NIHGNASESMLL.
    TIGRFAMsi TIGR00391. hydA. 1 hit.
    TIGR01409. TAT_signal_seq. 1 hit.
    PROSITEi PS51318. TAT. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Cloning and sequencing of the genes encoding the large and small subunits of the periplasmic (NiFeSe) hydrogenase of Desulfovibrio baculatus."
      Menon N.K., Peck H.D. Jr., le Gall J., Przybyla A.E.
      J. Bacteriol. 169:5401-5407(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. Erratum
      Menon N.K., Pect H.D. Jr., le Gall J., Przybyla A.E.
      J. Bacteriol. 170:4429-4429(1988)
      Cited for: SEQUENCE REVISION.
    3. Cited for: PROTEIN SEQUENCE OF 33-67.
      Strain: DSM 1743.
    4. "The crystal structure of a reduced [NiFeSe] hydrogenase provides an image of the activated catalytic center."
      Garcin E., Vernede X., Hatchikian E.C., Volbeda A., Frey M., Fontecilla-Camps J.-C.
      Structure 7:557-566(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS).

    Entry informationi

    Entry nameiPHSS_DESBA
    AccessioniPrimary (citable) accession number: P13063
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 1, 1990
    Last sequence update: January 1, 1990
    Last modified: October 1, 2014
    This is version 101 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Direct protein sequencing

    Documents

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

    External Data

    Dasty 3