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P13065

- PHSL_DESBA

UniProt

P13065 - PHSL_DESBA

Protein

Periplasmic [NiFeSe] hydrogenase large 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 87 (01 Oct 2014)
      Sequence version 3 (26 Feb 2008)
      Previous versions | rss
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    Functioni

    Catalytic activityi

    H2 + A = AH2.

    Cofactori

    Binds 2 irons ions. Iron 1 has 3 cyanide and carbon monoxide ligands. Iron 2 has 3 water ligands.
    Binds 1 nickel ion per subunit.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi52 – 521Iron 2
    Metal bindingi71 – 711Nickel
    Metal bindingi74 – 741Iron 1
    Metal bindingi74 – 741Nickel
    Metal bindingi445 – 4451Iron 2; via carbonyl oxygen
    Metal bindingi493 – 4931Nickel
    Metal bindingi496 – 4961Iron 1
    Metal bindingi496 – 4961Nickel
    Metal bindingi499 – 4991Iron 2

    GO - Molecular functioni

    1. ferredoxin hydrogenase activity Source: InterPro
    2. hydrogenase (acceptor) activity Source: UniProtKB-EC
    3. nickel cation binding Source: InterPro

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    Iron, Metal-binding, Nickel

    Names & Taxonomyi

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

    Subcellular locationi

    GO - Cellular componenti

    1. periplasmic space Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Periplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed
    Chaini2 – 514513Periplasmic [NiFeSe] hydrogenase large subunitPRO_0000199704Add
    BLAST

    Interactioni

    Subunit structurei

    Heterodimer of a large and a small subunit.

    Protein-protein interaction databases

    DIPiDIP-6125N.
    MINTiMINT-96867.

    Structurei

    Secondary structure

    1
    514
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi14 – 196
    Beta strandi22 – 254
    Beta strandi27 – 348
    Beta strandi37 – 459
    Helixi51 – 544
    Turni55 – 573
    Helixi60 – 623
    Helixi63 – 664
    Helixi67 – 704
    Beta strandi72 – 743
    Helixi75 – 9016
    Helixi96 – 12025
    Helixi123 – 1253
    Helixi145 – 1484
    Helixi152 – 18433
    Beta strandi185 – 1895
    Beta strandi191 – 1944
    Beta strandi197 – 2004
    Helixi204 – 22320
    Helixi225 – 23511
    Helixi237 – 2404
    Beta strandi249 – 2513
    Beta strandi254 – 2585
    Beta strandi264 – 2663
    Beta strandi269 – 2724
    Beta strandi275 – 2773
    Helixi281 – 2833
    Beta strandi284 – 2874
    Beta strandi296 – 2994
    Helixi303 – 3053
    Beta strandi323 – 3264
    Helixi335 – 3428
    Helixi348 – 35811
    Helixi365 – 3728
    Helixi375 – 39925
    Beta strandi414 – 42411
    Beta strandi427 – 43610
    Beta strandi439 – 4479
    Helixi449 – 4524
    Helixi464 – 4696
    Helixi481 – 4899
    Helixi494 – 4985

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1CC1X-ray2.15L2-499[»]
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP13065.

    Family & Domainsi

    Sequence similaritiesi

    Family and domain databases

    Gene3Di1.10.645.10. 1 hit.
    InterProiIPR001501. Ni-dep_hyd_lsu.
    IPR018194. Ni-dep_hyd_lsu_Ni_BS.
    IPR029014. NiFe_Hase-like.
    [Graphical view]
    PfamiPF00374. NiFeSe_Hases. 1 hit.
    [Graphical view]
    SUPFAMiSSF56762. SSF56762. 1 hit.
    PROSITEiPS00507. NI_HGENASE_L_1. 1 hit.
    PS00508. NI_HGENASE_L_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P13065-1 [UniParc]FASTAAdd to Basket

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    MSQAATPAAD GKVKISIDPL TRVEGHLKIE VEVKDGKVVD AKCSGGMFRG    50
    FEQILRGRDP RDSSQIVQRI CGVCPTAHCT ASVMAQDDAF GVKVTTNGRI 100
    TRNLIFGANY LQSHILHFYH LAALDYVKGP DVSPFVPRYA NADLLTDRIK 150
    DGAKADATNT YGLNQYLKAL EIRRICHEMV AMFGGRMPHV QGMVVGGATE 200
    IPTADKVAEY AARFKEVQKF VIEEYLPLIY TLGSVYTDLF ETGIGWKNVI 250
    AFGVFPEDDD YKTFLLKPGV YIDGKDEEFD SKLVKEYVGH SFFDHSAPGG 300
    LHYSVGETNP NPDKPGAYSF VKAPRYKDKP CEVGPLARMW VQNPELSPVG 350
    QKLLKELYGI EAKKFRDLGD KAFSIMGRHV LVAEETWLTA VAVEKWLKQV 400
    QPGAETYVKS EIPDAAEGTG FTEAPRGALL HYLKIKDKKI ENYQIVSATL 450
    WNANPRDDMG QRGPIEEALI GVPVPDIKNP VNVGRLVRSY DPULGCAVHV 500
    LHAETGEEHV VNID 514
    Length:514
    Mass (Da):56,862
    Last modified:February 26, 2008 - v3
    Checksum:iAC920132081C1ADC
    GO

    Non-standard residue

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Non-standard residuei493 – 4931Selenocysteine

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M18271 Genomic DNA. Translation: AAA23375.2.
    PIRiA33101. HQDVLB.

    Keywords - Coding sequence diversityi

    Selenocysteine

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M18271 Genomic DNA. Translation: AAA23375.2 .
    PIRi A33101. HQDVLB.

    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 L 2-499 [» ]
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-6125N.
    MINTi MINT-96867.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Miscellaneous databases

    EvolutionaryTracei P13065.

    Family and domain databases

    Gene3Di 1.10.645.10. 1 hit.
    InterProi IPR001501. Ni-dep_hyd_lsu.
    IPR018194. Ni-dep_hyd_lsu_Ni_BS.
    IPR029014. NiFe_Hase-like.
    [Graphical view ]
    Pfami PF00374. NiFeSe_Hases. 1 hit.
    [Graphical view ]
    SUPFAMi SSF56762. SSF56762. 1 hit.
    PROSITEi PS00507. NI_HGENASE_L_1. 1 hit.
    PS00508. NI_HGENASE_L_2. 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. "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), SELENOCYSTEINE AT SEC-493.

    Entry informationi

    Entry nameiPHSL_DESBA
    AccessioniPrimary (citable) accession number: P13065
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 1, 1990
    Last sequence update: February 26, 2008
    Last modified: October 1, 2014
    This is version 87 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Perhaps the leader of the small subunit serves as a transport vehicle for both subunits.

    Keywords - Technical termi

    3D-structure

    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