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P19066

- NIFD_RHISN

UniProt

P19066 - NIFD_RHISN

Protein

Nitrogenase molybdenum-iron protein alpha chain

Gene

nifD1

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Organism
Rhizobium sp. (strain NGR234)
Status
Reviewed - Annotation score: 4 out of 5- Protein inferred from homologyi
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    • History
      Entry version 98 (01 Oct 2014)
      Sequence version 2 (01 Nov 1997)
      Previous versions | rss
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    Functioni

    This molybdenum-iron protein is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation.

    Catalytic activityi

    8 reduced ferredoxin + 8 H+ + N2 + 16 ATP + 16 H2O = 8 oxidized ferredoxin + H2 + 2 NH3 + 16 ADP + 16 phosphate.

    Cofactori

    Binds 1 8Fe-7S cluster per heterodimer.By similarity
    Binds 1 7Fe-Mo-9S-C-homocitryl cluster per subunit.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi72 – 721Iron-sulfur (8Fe-7S); shared with beta chainBy similarity
    Metal bindingi98 – 981Iron-sulfur (8Fe-7S); shared with beta chainBy similarity
    Metal bindingi164 – 1641Iron-sulfur (8Fe-7S); shared with beta chainBy similarity
    Metal bindingi287 – 2871Molybdenum-iron-sulfur-carbon (7Fe-Mo-9S-C-homocitryl)By similarity
    Metal bindingi454 – 4541Molybdenum-iron-sulfur-carbon (7Fe-Mo-9S-C-homocitryl); via pros nitrogenBy similarity

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-KW
    2. carbonyl sulfide nitrogenase activity Source: UniProtKB-EC
    3. iron-sulfur cluster binding Source: UniProtKB-KW
    4. metal ion binding Source: UniProtKB-KW
    5. nitrogenase activity Source: UniProtKB-EC

    GO - Biological processi

    1. nitrogen fixation Source: UniProtKB-KW

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Nitrogen fixation

    Keywords - Ligandi

    ATP-binding, Iron, Iron-sulfur, Metal-binding, Molybdenum, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciRETL1328306-WGS:GSTH-5560-MONOMER.
    SFRE394:GBYN-6139-MONOMER.
    SFRE394:GBYN-6163-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Nitrogenase molybdenum-iron protein alpha chain (EC:1.18.6.1)
    Alternative name(s):
    Dinitrogenase
    Nitrogenase component I
    Gene namesi
    Name:nifD1
    Ordered Locus Names:NGR_a01120
    ORF Names:y4vL
    AND
    Name:nifD2
    Ordered Locus Names:NGR_a00880
    ORF Names:y4xB
    Encoded oniPlasmid sym pNGR234a0 Publication
    OrganismiRhizobium sp. (strain NGR234)
    Taxonomic identifieri394 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesRhizobiaceaeSinorhizobium/Ensifer groupSinorhizobium
    ProteomesiUP000001054: Plasmid sym pNGR234a

    Subcellular locationi

    GO - Cellular componenti

    1. molybdenum-iron nitrogenase complex Source: InterPro

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 504504Nitrogenase molybdenum-iron protein alpha chainPRO_0000153079Add
    BLAST

    Interactioni

    Subunit structurei

    Tetramer of two alpha and two beta chains. Forms complex with the iron protein (nitrogenase component 2).

    Protein-protein interaction databases

    STRINGi394.NGR_a01120.

    Structurei

    3D structure databases

    ProteinModelPortaliP19066.
    SMRiP19066. Positions 13-492.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the NifD/NifK/NifE/NifN family.Curated

    Phylogenomic databases

    eggNOGiCOG2710.
    HOGENOMiHOG000005528.
    KOiK02586.
    OMAiIDTFVTM.
    OrthoDBiEOG6VHZ72.

    Family and domain databases

    InterProiIPR000510. Nase/OxRdtase_comp1.
    IPR010143. Nase_comp1_asu.
    IPR000318. Nase_comp1_CS.
    IPR005972. Nase_Mo-Fe_asu.
    [Graphical view]
    PfamiPF00148. Oxidored_nitro. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR01862. N2-ase-Ialpha. 1 hit.
    TIGR01282. nifD. 1 hit.
    PROSITEiPS00699. NITROGENASE_1_1. 1 hit.
    PS00090. NITROGENASE_1_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P19066-1 [UniParc]FASTAAdd to Basket

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    MSLDYENDSA LHQELITQVL SQYPHKAAKR RQKHLSVASD REAVGEEGET    50
    LSECDVKSNI KSIPGVMTIR GCAYAGSKGV VWGPVKDMVH ISHGPVGCGQ 100
    YSWSQRRNYY VGTTGVDTFV TMQFTSDFQE KDIVFGGDKK LEQVIDEIEE 150
    LFPLNNGITI QSECPIGLIG DDIEAVSRKK AAEHETTIVP VRCEGFRGVS 200
    QSLGHHIAND AIRDWVFDKA DGKTDVEFET GPYDVNVIGD YNIGGDAWAS 250
    RILLEEIGLR VVGNWSGDAT LAEVERAPRA KLNLIHCYRS MNYICRHMEE 300
    RYAIPWMEYN FFGPSQIEAS LRKIARHFGP TIEERAERVI AKYRPLVDAV 350
    IDKYWPRLQG KRVMLYVGGL RPRHVITAYE DLGMQIVGTG YEFAHNDDYQ 400
    RTGHYVKTGT LIYDDATSYE LDTFIERIRP DLVGSGIKEK YPVQKMGIPF 450
    RQMHSWDYSG PYHGYDGFAI FARDMDLAIN NPVWDLYDAP WKKMTVPTAA 500
    VAAE 504
    Length:504
    Mass (Da):56,944
    Last modified:November 1, 1997 - v2
    Checksum:iD3BE3291A9D276DC
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti201 – 2011Q → K in AAA26328. (PubMed:2744485)Curated
    Sequence conflicti303 – 3031A → G in AAA26328. (PubMed:2744485)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U00090 Genomic DNA. Translation: AAB91900.1.
    U00090 Genomic DNA. Translation: AAB91924.1.
    M26961 Genomic DNA. Translation: AAA26330.1.
    M26962 Genomic DNA. Translation: AAA26328.1.
    PIRiPS0045.
    T10829.
    RefSeqiNP_444113.1. NC_000914.2.
    NP_444137.1. NC_000914.2.
    WP_010875129.1. NC_000914.2.

    Genome annotation databases

    EnsemblBacteriaiAAB91900; AAB91900; NGR_a01120.
    AAB91924; AAB91924; NGR_a00880.
    GeneIDi962482.
    962502.
    KEGGirhi:NGR_a00880.
    rhi:NGR_a01120.
    PATRICi32300883. VBIRhiSp122450_0077.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U00090 Genomic DNA. Translation: AAB91900.1 .
    U00090 Genomic DNA. Translation: AAB91924.1 .
    M26961 Genomic DNA. Translation: AAA26330.1 .
    M26962 Genomic DNA. Translation: AAA26328.1 .
    PIRi PS0045.
    T10829.
    RefSeqi NP_444113.1. NC_000914.2.
    NP_444137.1. NC_000914.2.
    WP_010875129.1. NC_000914.2.

    3D structure databases

    ProteinModelPortali P19066.
    SMRi P19066. Positions 13-492.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 394.NGR_a01120.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAB91900 ; AAB91900 ; NGR_a01120 .
    AAB91924 ; AAB91924 ; NGR_a00880 .
    GeneIDi 962482.
    962502.
    KEGGi rhi:NGR_a00880.
    rhi:NGR_a01120.
    PATRICi 32300883. VBIRhiSp122450_0077.

    Phylogenomic databases

    eggNOGi COG2710.
    HOGENOMi HOG000005528.
    KOi K02586.
    OMAi IDTFVTM.
    OrthoDBi EOG6VHZ72.

    Enzyme and pathway databases

    BioCyci RETL1328306-WGS:GSTH-5560-MONOMER.
    SFRE394:GBYN-6139-MONOMER.
    SFRE394:GBYN-6163-MONOMER.

    Family and domain databases

    InterProi IPR000510. Nase/OxRdtase_comp1.
    IPR010143. Nase_comp1_asu.
    IPR000318. Nase_comp1_CS.
    IPR005972. Nase_Mo-Fe_asu.
    [Graphical view ]
    Pfami PF00148. Oxidored_nitro. 1 hit.
    [Graphical view ]
    TIGRFAMsi TIGR01862. N2-ase-Ialpha. 1 hit.
    TIGR01282. nifD. 1 hit.
    PROSITEi PS00699. NITROGENASE_1_1. 1 hit.
    PS00090. NITROGENASE_1_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Molecular basis of symbiosis between Rhizobium and legumes."
      Freiberg C.A., Fellay R., Bairoch A., Broughton W.J., Rosenthal A., Perret X.
      Nature 387:394-401(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: NGR234.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: NGR234.
    3. "Structural and functional analysis of nitrogenase genes from the broad-host-range Rhizobium strain ANU240."
      Badenoch-Jones J., Holton T.A., Morrison C.M., Scott K.F., Shine J.
      Gene 77:141-153(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-16 AND 199-393.
      Strain: ANU 240.

    Entry informationi

    Entry nameiNIFD_RHISN
    AccessioniPrimary (citable) accession number: P19066
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1990
    Last sequence update: November 1, 1997
    Last modified: October 1, 2014
    This is version 98 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Plasmid, Reference proteome

    Documents

    1. Rhizobium plasmid pNGR234a
      Rhizobium plasmid pNGR234a: entries and gene names
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3