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P21852

- PHNL_DESVM

UniProt

P21852 - PHNL_DESVM

Protein

Periplasmic [NiFe] hydrogenase large subunit

Gene

hydB

Organism
Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 95 (01 Oct 2014)
      Sequence version 2 (14 Apr 2009)
      Previous versions | rss
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    Functioni

    Catalyzes the reversible oxidoreduction of molecular hydrogen, in conjunction with a specific electron acceptor, cytochrome c3.

    Catalytic activityi

    2 H2 + ferricytochrome c3 = 4 H+ + ferrocytochrome c3.

    Cofactori

    Nickel.
    Iron.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi62 – 621Magnesium
    Metal bindingi81 – 811Nickel
    Metal bindingi84 – 841Iron
    Metal bindingi84 – 841Nickel
    Metal bindingi498 – 4981Magnesium; via carbonyl oxygen
    Metal bindingi546 – 5461Nickel
    Metal bindingi549 – 5491Iron
    Metal bindingi549 – 5491Nickel
    Metal bindingi552 – 5521Magnesium; via tele nitrogen

    GO - Molecular functioni

    1. cytochrome-c3 hydrogenase activity Source: UniProtKB-EC
    2. ferredoxin hydrogenase activity Source: InterPro
    3. nickel cation binding Source: InterPro

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    Iron, Magnesium, Metal-binding, Nickel

    Enzyme and pathway databases

    BioCyciDVUL883:GCJ5-285-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Periplasmic [NiFe] hydrogenase large subunit (EC:1.12.2.1)
    Alternative name(s):
    NiFe hydrogenlyase large chain
    Gene namesi
    Name:hydB
    Ordered Locus Names:DvMF_0270
    OrganismiDesulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
    Taxonomic identifieri883 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio
    ProteomesiUP000001361: Chromosome

    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
    Chaini1 – 552552Periplasmic [NiFe] hydrogenase large subunitPRO_0000013405Add
    BLAST
    Propeptidei553 – 56715PRO_0000013406Add
    BLAST

    Interactioni

    Subunit structurei

    Heterodimer of a large and a small subunit.

    Protein-protein interaction databases

    MINTiMINT-247638.
    STRINGi883.DvMF_0270.

    Structurei

    Secondary structure

    1
    567
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi23 – 297
    Beta strandi32 – 354
    Beta strandi37 – 448
    Beta strandi47 – 559
    Helixi61 – 655
    Helixi70 – 723
    Helixi73 – 786
    Beta strandi82 – 843
    Helixi87 – 10014
    Helixi106 – 13025
    Helixi133 – 1353
    Helixi140 – 1445
    Helixi147 – 15711
    Beta strandi158 – 1603
    Helixi164 – 17916
    Helixi184 – 1863
    Turni190 – 1934
    Helixi202 – 23029
    Beta strandi233 – 2353
    Helixi247 – 2504
    Helixi252 – 27120
    Helixi273 – 28311
    Helixi285 – 2895
    Beta strandi296 – 30510
    Helixi309 – 3113
    Beta strandi312 – 3209
    Helixi324 – 3263
    Helixi332 – 3343
    Beta strandi335 – 3384
    Turni340 – 3434
    Beta strandi344 – 3474
    Helixi352 – 3543
    Beta strandi371 – 3733
    Beta strandi375 – 3784
    Helixi387 – 39610
    Helixi400 – 41314
    Helixi417 – 4204
    Helixi423 – 45331
    Beta strandi467 – 47711
    Beta strandi480 – 48910
    Beta strandi492 – 4998
    Helixi501 – 5066
    Helixi517 – 5226
    Beta strandi530 – 5323
    Helixi534 – 5429
    Helixi547 – 5515

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1H2AX-ray1.80L1-567[»]
    1H2RX-ray1.40L19-552[»]
    1UBHX-ray1.35L19-552[»]
    1UBJX-ray1.35L19-552[»]
    1UBKX-ray1.18L19-552[»]
    1UBLX-ray1.20L19-552[»]
    1UBMX-ray1.40L19-552[»]
    1UBOX-ray1.35L19-552[»]
    1UBRX-ray1.34L19-552[»]
    1UBTX-ray1.34L19-552[»]
    1UBUX-ray1.35L19-552[»]
    1WUHX-ray1.24L19-552[»]
    1WUIX-ray1.04L19-552[»]
    1WUJX-ray1.40L19-552[»]
    1WUKX-ray1.10L19-552[»]
    1WULX-ray1.50L19-552[»]
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP21852.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0374.
    HOGENOMiHOG000278799.
    KOiK00437.
    OMAiWEMPDEA.
    OrthoDBiEOG6M9DSB.

    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.

    P21852-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSGCRAQNAP GGIPVTPKSS YSGPIVVDPV TRIEGHLRIE VEVENGKVKN    50
    AYSSSTLFRG LEIILKGRDP RDAQHFTQRT CGVCTYTHAL ASTRCVDNAV 100
    GVHIPKNATY IRNLVLGAQY LHDHIVHFYH LHALDFVDVT AALKADPAKA 150
    AKVASSISPR KTTAADLKAV QDKLKTFVES GQLGPFTNAY FLGGHPAYYL 200
    DPETNLIATA HYLEALRLQV KAARAMAVFG AKNPHTQFTV VGGVTCYDAL 250
    TPQRIAEFEA LWKETKAFVD EVYIPDLLVV AAAYKDWTQY GGTDNFITFG 300
    EFPKDEYDLN SRFFKPGVVF KRDFKNIKPF DKMQIEEHVR HSWYEGAEAR 350
    HPWKGQTQPK YTDLHGDDRY SWMKAPRYMG EPMETGPLAQ VLIAYSQGHP 400
    KVKAVTDAVL AKLGVGPEAL FSTLGRTAAR GIETAVIAEY VGVMLQEYKD 450
    NIAKGDNVIC APWEMPKQAE GVGFVNAPRG GLSHWIRIED GKIGNFQLVV 500
    PSTWTLGPRC DKNKLSPVEA SLIGTPVADA KRPVEILRTV HSFDPCIACG 550
    VHVIDGHTNE VHKFRIL 567
    Length:567
    Mass (Da):62,641
    Last modified:April 14, 2009 - v2
    Checksum:i8BE92277C0E46FDA
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti180 – 1801S → T in AAA23370. (PubMed:2269874)Curated
    Sequence conflicti514 – 5152KL → NV in AAA23370. (PubMed:2269874)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M58339 Genomic DNA. Translation: AAA23370.1.
    CP001197 Genomic DNA. Translation: ACL07227.1.
    PIRiB45865.
    RefSeqiWP_012611421.1. NC_011769.1.
    YP_002434695.1. NC_011769.1.

    Genome annotation databases

    EnsemblBacteriaiACL07227; ACL07227; DvMF_0270.
    GeneIDi7172152.
    KEGGidvm:DvMF_0270.
    PATRICi21770453. VBIDesVul86729_0281.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M58339 Genomic DNA. Translation: AAA23370.1 .
    CP001197 Genomic DNA. Translation: ACL07227.1 .
    PIRi B45865.
    RefSeqi WP_012611421.1. NC_011769.1.
    YP_002434695.1. NC_011769.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1H2A X-ray 1.80 L 1-567 [» ]
    1H2R X-ray 1.40 L 19-552 [» ]
    1UBH X-ray 1.35 L 19-552 [» ]
    1UBJ X-ray 1.35 L 19-552 [» ]
    1UBK X-ray 1.18 L 19-552 [» ]
    1UBL X-ray 1.20 L 19-552 [» ]
    1UBM X-ray 1.40 L 19-552 [» ]
    1UBO X-ray 1.35 L 19-552 [» ]
    1UBR X-ray 1.34 L 19-552 [» ]
    1UBT X-ray 1.34 L 19-552 [» ]
    1UBU X-ray 1.35 L 19-552 [» ]
    1WUH X-ray 1.24 L 19-552 [» ]
    1WUI X-ray 1.04 L 19-552 [» ]
    1WUJ X-ray 1.40 L 19-552 [» ]
    1WUK X-ray 1.10 L 19-552 [» ]
    1WUL X-ray 1.50 L 19-552 [» ]
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    MINTi MINT-247638.
    STRINGi 883.DvMF_0270.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ACL07227 ; ACL07227 ; DvMF_0270 .
    GeneIDi 7172152.
    KEGGi dvm:DvMF_0270.
    PATRICi 21770453. VBIDesVul86729_0281.

    Phylogenomic databases

    eggNOGi COG0374.
    HOGENOMi HOG000278799.
    KOi K00437.
    OMAi WEMPDEA.
    OrthoDBi EOG6M9DSB.

    Enzyme and pathway databases

    BioCyci DVUL883:GCJ5-285-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P21852.

    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 a [NiFe] hydrogenase operon from Desulfovibrio vulgaris Miyazaki F."
      Deckers H.M., Wilson F.R., Voordouw G.
      J. Gen. Microbiol. 136:2021-2028(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Complete sequence of Desulfovibrio vulgaris str. 'Miyazaki F'."
      Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Sims D., Brettin T., Detter J.C., Han C., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Hazen T.C., Richardson P.
      Submitted (OCT-2008) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: Miyazaki F / DSM 19637.
    3. "Unusual ligand structure in Ni-Fe active center and an additional Mg site in hydrogenase revealed by high resolution X-ray structure analysis."
      Higuchi Y., Yagi T., Yasuoka N.
      Structure 5:1671-1680(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 19-552.
    4. "Removal of the bridging ligand atom at the Ni-Fe active site of [NiFe] hydrogenase upon reduction with H2, as revealed by X-ray structure analysis at 1.4 A resolution."
      Higuchi Y., Ogata H., Miki K., Yasuoka N., Yagi T.
      Structure 7:549-556(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS).

    Entry informationi

    Entry nameiPHNL_DESVM
    AccessioniPrimary (citable) accession number: P21852
    Secondary accession number(s): B8DPE0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 1, 1991
    Last sequence update: April 14, 2009
    Last modified: October 1, 2014
    This is version 95 of the entry and version 2 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, Complete proteome, Reference proteome

    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