Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Basket 0
(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

P07598

- PHFL_DESVH

UniProt

P07598 - PHFL_DESVH

Protein

Periplasmic [Fe] hydrogenase large subunit

Gene

hydA

Organism
Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
    • BLAST
    • Align
    • Format
    • Add to basket
    • History
      Entry version 123 (01 Oct 2014)
      Sequence version 1 (01 Apr 1988)
      Previous versions | rss
    • Help video
    • Feedback
    • Comment

    Functioni

    May be involved in hydrogen uptake for the reduction of sulfate to hydrogen sulfide in an electron transport chain. Cytochrome c3 is likely to be the physiological electron carrier for the enzyme.

    Catalytic activityi

    H2 + 2 oxidized ferredoxin = 2 reduced ferredoxin + 2 H+.

    Cofactori

    Binds 3 4Fe-4S clusters per subunit.
    Binds 2 iron ions per subunit.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi35 – 351Iron-sulfur 1 (4Fe-4S)
    Metal bindingi38 – 381Iron-sulfur 1 (4Fe-4S)
    Metal bindingi41 – 411Iron-sulfur 1 (4Fe-4S)
    Metal bindingi45 – 451Iron-sulfur 2 (4Fe-4S)
    Metal bindingi66 – 661Iron-sulfur 2 (4Fe-4S)
    Metal bindingi69 – 691Iron-sulfur 2 (4Fe-4S)
    Metal bindingi72 – 721Iron-sulfur 2 (4Fe-4S)
    Metal bindingi76 – 761Iron-sulfur 1 (4Fe-4S)
    Metal bindingi179 – 1791Iron-sulfur 3 (4Fe-4S)
    Metal bindingi234 – 2341Iron-sulfur 3 (4Fe-4S)
    Metal bindingi378 – 3781Iron-sulfur 3 (4Fe-4S)
    Metal bindingi382 – 3821Diiron subcluster
    Metal bindingi382 – 3821Iron-sulfur 3 (4Fe-4S)

    GO - Molecular functioni

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

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Electron transport, Transport

    Keywords - Ligandi

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

    Enzyme and pathway databases

    BioCyciDVUL882:GJIL-1810-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Periplasmic [Fe] hydrogenase large subunit (EC:1.12.7.2)
    Alternative name(s):
    Fe hydrogenlyase
    Gene namesi
    Name:hydA
    Ordered Locus Names:DVU_1769
    OrganismiDesulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)
    Taxonomic identifieri882 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio
    ProteomesiUP000002194: 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 – 421421Periplasmic [Fe] hydrogenase large subunitPRO_0000159239Add
    BLAST

    Interactioni

    Subunit structurei

    Heterodimer of a large and a small subunit.

    Protein-protein interaction databases

    DIPiDIP-6186N.
    STRINGi882.DVU1769.

    Structurei

    Secondary structure

    1
    421
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi4 – 63
    Beta strandi9 – 113
    Helixi22 – 243
    Beta strandi27 – 304
    Turni32 – 343
    Helixi40 – 445
    Helixi63 – 653
    Helixi73 – 753
    Beta strandi81 – 844
    Helixi88 – 969
    Beta strandi101 – 1066
    Helixi108 – 1125
    Helixi114 – 1185
    Helixi127 – 13711
    Beta strandi140 – 1423
    Helixi145 – 16420
    Beta strandi172 – 1754
    Helixi180 – 18910
    Helixi191 – 1966
    Helixi203 – 2119
    Helixi214 – 2196
    Helixi223 – 2253
    Beta strandi226 – 2338
    Helixi236 – 2416
    Beta strandi256 – 2594
    Helixi260 – 26910
    Helixi274 – 2763
    Turni284 – 2863
    Helixi291 – 2944
    Helixi295 – 2973
    Helixi301 – 31515
    Helixi325 – 3273
    Beta strandi332 – 3409
    Beta strandi343 – 35210
    Helixi353 – 3553
    Helixi356 – 3649
    Beta strandi371 – 3788
    Helixi382 – 3843

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1E08NMR-A27-397[»]
    1GX7NMR-A27-397[»]
    1HFEX-ray1.60L/M1-421[»]
    DisProtiDP00108.
    ProteinModelPortaliP07598.
    SMRiP07598. Positions 2-397.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP07598.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini26 – 57324Fe-4S ferredoxin-type 1PROSITE-ProRule annotationAdd
    BLAST
    Domaini59 – 86284Fe-4S ferredoxin-type 2PROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Contains 2 4Fe-4S ferredoxin-type domains.PROSITE-ProRule annotation

    Keywords - Domaini

    Repeat

    Phylogenomic databases

    eggNOGiCOG4624.
    KOiK00533.
    OMAiIFTVSVM.
    OrthoDBiEOG6CVV7G.
    PhylomeDBiP07598.

    Family and domain databases

    InterProiIPR001450. 4Fe4S-bd_dom.
    IPR017896. 4Fe4S_Fe-S-bd.
    IPR017900. 4Fe4S_Fe_S_CS.
    IPR009016. Fe_hydrogenase.
    IPR004108. Fe_hydrogenase_lsu_C.
    IPR013352. Fe_hydrogenase_subset.
    [Graphical view]
    PfamiPF02906. Fe_hyd_lg_C. 1 hit.
    PF00037. Fer4. 2 hits.
    [Graphical view]
    SUPFAMiSSF53920. SSF53920. 1 hit.
    TIGRFAMsiTIGR02512. FeFe_hydrog_A. 1 hit.
    PROSITEiPS00198. 4FE4S_FER_1. 2 hits.
    PS51379. 4FE4S_FER_2. 2 hits.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P07598-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSRTVMERIE YEMHTPDPKA DPDKLHFVQI DEAKCIGCDT CSQYCPTAAI    50
    FGEMGEPHSI PHIEACINCG QCLTHCPENA IYEAQSWVPE VEKKLKDGKV 100
    KCIAMPAPAV RYALGDAFGM PVGSVTTGKM LAALQKLGFA HCWDTEFTAD 150
    VTIWEEGSEF VERLTKKSDM PLPQFTSCCP GWQKYAETYY PELLPHFSTC 200
    KSPIGMNGAL AKTYGAERMK YDPKQVYTVS IMPCIAKKYE GLRPELKSSG 250
    MRDIDATLTT RELAYMIKKA GIDFAKLPDG KRDSLMGEST GGATIFGVTG 300
    GVMEAALRFA YEAVTGKKPD SWDFKAVRGL DGIKEATVNV GGTDVKVAVV 350
    HGAKRFKQVC DDVKAGKSPY HFIEYMACPG GCVCGGGQPV MPGVLEAMDR 400
    TTTRLYAGLK KRLAMASANK A 421
    Length:421
    Mass (Da):45,951
    Last modified:April 1, 1988 - v1
    Checksum:i8E70A0775B68AACD
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti35 – 351C → K AA sequence (PubMed:3322275)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X02416 Genomic DNA. Translation: CAA26266.1.
    AE017285 Genomic DNA. Translation: AAS96246.1.
    Z15142 Genomic DNA. Translation: CAA78848.1.
    PIRiA24551. HQDVFL.
    RefSeqiYP_010987.1. NC_002937.3.

    Genome annotation databases

    EnsemblBacteriaiAAS96246; AAS96246; DVU_1769.
    GeneIDi2795816.
    KEGGidvu:DVU1769.
    PATRICi32063304. VBIDesVul119526_1625.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X02416 Genomic DNA. Translation: CAA26266.1 .
    AE017285 Genomic DNA. Translation: AAS96246.1 .
    Z15142 Genomic DNA. Translation: CAA78848.1 .
    PIRi A24551. HQDVFL.
    RefSeqi YP_010987.1. NC_002937.3.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1E08 NMR - A 27-397 [» ]
    1GX7 NMR - A 27-397 [» ]
    1HFE X-ray 1.60 L/M 1-421 [» ]
    DisProti DP00108.
    ProteinModelPortali P07598.
    SMRi P07598. Positions 2-397.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-6186N.
    STRINGi 882.DVU1769.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAS96246 ; AAS96246 ; DVU_1769 .
    GeneIDi 2795816.
    KEGGi dvu:DVU1769.
    PATRICi 32063304. VBIDesVul119526_1625.

    Phylogenomic databases

    eggNOGi COG4624.
    KOi K00533.
    OMAi IFTVSVM.
    OrthoDBi EOG6CVV7G.
    PhylomeDBi P07598.

    Enzyme and pathway databases

    BioCyci DVUL882:GJIL-1810-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P07598.

    Family and domain databases

    InterProi IPR001450. 4Fe4S-bd_dom.
    IPR017896. 4Fe4S_Fe-S-bd.
    IPR017900. 4Fe4S_Fe_S_CS.
    IPR009016. Fe_hydrogenase.
    IPR004108. Fe_hydrogenase_lsu_C.
    IPR013352. Fe_hydrogenase_subset.
    [Graphical view ]
    Pfami PF02906. Fe_hyd_lg_C. 1 hit.
    PF00037. Fer4. 2 hits.
    [Graphical view ]
    SUPFAMi SSF53920. SSF53920. 1 hit.
    TIGRFAMsi TIGR02512. FeFe_hydrog_A. 1 hit.
    PROSITEi PS00198. 4FE4S_FER_1. 2 hits.
    PS51379. 4FE4S_FER_2. 2 hits.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Nucleotide sequence of the gene encoding the hydrogenase from Desulfovibrio vulgaris (Hildenborough)."
      Voordouw G., Brenner S.
      Eur. J. Biochem. 148:515-520(1985) [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. Cited for: PROTEIN SEQUENCE OF 1-35.
    4. van den Berg W.A.M., Stokkermans J.P.W.G., van Dongen W.M.A.M.
      Submitted (SEP-1992) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-15.
    5. "Mossbauer characterization of the iron-sulfur clusters in Desulfovibrio vulgaris hydrogenase."
      Pereira A.S., Tavares P., Moura I., Moura J.J.G., Huynh B.H.
      J. Am. Chem. Soc. 123:2771-2782(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: MOSSBAUER SPECTROSCOPY OF IRON-SULFUR CLUSTERS.
    6. "Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual coordination to an active site Fe binuclear center."
      Nicolet Y., Piras C., Legrand P., Hatchikian E.C., Fontecilla-Camps J.-C.
      Structure 7:13-23(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
    7. "Crystallographic and FTIR spectroscopic evidence of changes in Fe coordination upon reduction of the active site of the Fe-only hydrogenase from Desulfovibrio desulfuricans."
      Nicolet Y., de Lacey A.L., Vernede X., Fernandez V.M., Hatchikian E.C., Fontecilla-Camps J.-C.
      J. Am. Chem. Soc. 123:1596-1601(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS), ABSORPTION SPECTROSCOPY, EPR SPECTROSCOPY, FOURIER-TRANSFORM INFRARED SPECTROSCOPY.

    Entry informationi

    Entry nameiPHFL_DESVH
    AccessioniPrimary (citable) accession number: P07598
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 1, 1988
    Last sequence update: April 1, 1988
    Last modified: October 1, 2014
    This is version 123 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    [Fe], [NiFe], and [NiFeSe] hydrogenases appear to represent three distinct enzymes having hydrogenase activity.

    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

    External Data

    Dasty 3