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P07328

- NIFD_AZOVI

UniProt

P07328 - NIFD_AZOVI

Protein

Nitrogenase molybdenum-iron protein alpha chain

Gene

nifD

Organism
Azotobacter vinelandii
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 101 (01 Oct 2014)
      Sequence version 3 (23 Jan 2007)
      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.
    Binds 1 7Fe-Mo-9S-C-homocitryl cluster per subunit.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi62 – 621Iron-sulfur (8Fe-7S); shared with beta chain
    Metal bindingi88 – 881Iron-sulfur (8Fe-7S); shared with beta chain
    Metal bindingi154 – 1541Iron-sulfur (8Fe-7S); shared with beta chain
    Metal bindingi275 – 2751Molybdenum-iron-sulfur-carbon (7Fe-Mo-9S-C-homocitryl)
    Metal bindingi442 – 4421Molybdenum-iron-sulfur-carbon (7Fe-Mo-9S-C-homocitryl); via pros nitrogen

    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

    BioCyciMetaCyc:MONOMER-16520.

    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:nifD
    OrganismiAzotobacter vinelandii
    Taxonomic identifieri354 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaeAzotobacter

    Subcellular locationi

    GO - Cellular componenti

    1. molybdenum-iron nitrogenase complex Source: InterPro

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi195 – 1951H → Q: No nitrogenase activity.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 492491Nitrogenase molybdenum-iron protein alpha chainPRO_0000153058Add
    BLAST

    Interactioni

    Subunit structurei

    Tetramer of two alpha and two beta chains. Forms complex with the iron protein (nitrogenase component 2).8 Publications

    Protein-protein interaction databases

    DIPiDIP-6252N.
    MINTiMINT-1508543.

    Structurei

    Secondary structure

    1
    492
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi6 – 1712
    Helixi22 – 298
    Beta strandi32 – 343
    Helixi42 – 443
    Helixi63 – 675
    Helixi68 – 725
    Beta strandi78 – 869
    Helixi87 – 915
    Turni92 – 943
    Turni104 – 1063
    Beta strandi110 – 1123
    Helixi120 – 1256
    Helixi128 – 14114
    Beta strandi148 – 1525
    Helixi155 – 1584
    Helixi163 – 17412
    Beta strandi178 – 1814
    Beta strandi187 – 1904
    Helixi191 – 20515
    Turni206 – 2127
    Beta strandi222 – 2287
    Turni232 – 2354
    Helixi236 – 2449
    Beta strandi248 – 2547
    Helixi259 – 2646
    Helixi265 – 2673
    Beta strandi269 – 2746
    Helixi276 – 29015
    Beta strandi294 – 2963
    Helixi302 – 31312
    Helixi318 – 34629
    Beta strandi350 – 3534
    Beta strandi355 – 3584
    Helixi359 – 3624
    Helixi364 – 3685
    Turni369 – 3713
    Beta strandi373 – 3819
    Helixi384 – 3918
    Beta strandi399 – 4035
    Helixi406 – 41611
    Beta strandi419 – 4235
    Helixi425 – 4339
    Beta strandi438 – 4436
    Helixi444 – 4463
    Helixi452 – 46716
    Helixi470 – 4734
    Beta strandi475 – 4773

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1FP4X-ray2.50A/C1-492[»]
    1G20X-ray2.20A/C1-492[»]
    1G21X-ray3.00A/C1-492[»]
    1L5HX-ray2.30A2-492[»]
    1M1NX-ray1.16A/C/E/G2-492[»]
    1M1YX-ray3.20A/C/I/K2-492[»]
    1M34X-ray2.30A/C/I/K2-492[»]
    1N2CX-ray3.00A/C2-492[»]
    2AFHX-ray2.10A/C2-492[»]
    2AFIX-ray3.10A/C/I/K2-492[»]
    2AFKX-ray2.30A/C2-492[»]
    2MINX-ray2.03A/C2-492[»]
    3K1AX-ray2.23A/C2-492[»]
    3MINX-ray2.03A/C2-492[»]
    3U7QX-ray1.00A/C1-492[»]
    4ND8X-ray2.00A/C1-492[»]
    ProteinModelPortaliP07328.
    SMRiP07328. Positions 4-481.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP07328.

    Family & Domainsi

    Sequence similaritiesi

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

    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.

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

    P07328-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTGMSREEVE SLIQEVLEVY PEKARKDRNK HLAVNDPAVT QSKKCIISNK    50
    KSQPGLMTIR GCAYAGSKGV VWGPIKDMIH ISHGPVGCGQ YSRAGRRNYY 100
    IGTTGVNAFV TMNFTSDFQE KDIVFGGDKK LAKLIDEVET LFPLNKGISV 150
    QSECPIGLIG DDIESVSKVK GAELSKTIVP VRCEGFRGVS QSLGHHIAND 200
    AVRDWVLGKR DEDTTFASTP YDVAIIGDYN IGGDAWSSRI LLEEMGLRCV 250
    AQWSGDGSIS EIELTPKVKL NLVHCYRSMN YISRHMEEKY GIPWMEYNFF 300
    GPTKTIESLR AIAAKFDESI QKKCEEVIAK YKPEWEAVVA KYRPRLEGKR 350
    VMLYIGGLRP RHVIGAYEDL GMEVVGTGYE FAHNDDYDRT MKEMGDSTLL 400
    YDDVTGYEFE EFVKRIKPDL IGSGIKEKFI FQKMGIPFRE MHSWDYSGPY 450
    HGFDGFAIFA RDMDMTLNNP CWKKLQAPWE ASEGAEKVAA SA 492
    Length:492
    Mass (Da):55,289
    Last modified:January 23, 2007 - v3
    Checksum:i7D4B2CF5E99664D7
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti3 – 31G → R in AAA22143. (PubMed:3863780)Curated
    Sequence conflicti190 – 1901S → C in AAA22143. (PubMed:3863780)Curated
    Sequence conflicti212 – 2121E → A in AAA22143. (PubMed:3863780)Curated
    Sequence conflicti258 – 2614SISE → YISQ(PubMed:3863780)Curated
    Sequence conflicti407 – 4071Y → M in AAA22143. (PubMed:3863780)Curated
    Sequence conflicti440 – 4401E → Q(PubMed:2644218)Curated
    Sequence conflicti440 – 4401E → Q(PubMed:3863780)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M20568 Genomic DNA. Translation: AAA64710.1.
    M11579 Genomic DNA. Translation: AAA22143.1.
    X06886 Genomic DNA. Translation: CAA30004.1.
    PIRiA43049. NIAVMA.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M20568 Genomic DNA. Translation: AAA64710.1 .
    M11579 Genomic DNA. Translation: AAA22143.1 .
    X06886 Genomic DNA. Translation: CAA30004.1 .
    PIRi A43049. NIAVMA.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1FP4 X-ray 2.50 A/C 1-492 [» ]
    1G20 X-ray 2.20 A/C 1-492 [» ]
    1G21 X-ray 3.00 A/C 1-492 [» ]
    1L5H X-ray 2.30 A 2-492 [» ]
    1M1N X-ray 1.16 A/C/E/G 2-492 [» ]
    1M1Y X-ray 3.20 A/C/I/K 2-492 [» ]
    1M34 X-ray 2.30 A/C/I/K 2-492 [» ]
    1N2C X-ray 3.00 A/C 2-492 [» ]
    2AFH X-ray 2.10 A/C 2-492 [» ]
    2AFI X-ray 3.10 A/C/I/K 2-492 [» ]
    2AFK X-ray 2.30 A/C 2-492 [» ]
    2MIN X-ray 2.03 A/C 2-492 [» ]
    3K1A X-ray 2.23 A/C 2-492 [» ]
    3MIN X-ray 2.03 A/C 2-492 [» ]
    3U7Q X-ray 1.00 A/C 1-492 [» ]
    4ND8 X-ray 2.00 A/C 1-492 [» ]
    ProteinModelPortali P07328.
    SMRi P07328. Positions 4-481.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-6252N.
    MINTi MINT-1508543.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Enzyme and pathway databases

    BioCyci MetaCyc:MONOMER-16520.

    Miscellaneous databases

    EvolutionaryTracei P07328.

    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. "Physical and genetic map of the major nif gene cluster from Azotobacter vinelandii."
      Jacobson M.R., Brigle K.E., Bennett L.T., Setterquist R.A., Wilson M.S., Cash V.L., Beynon J., Newton W.E., Dean D.R.
      J. Bacteriol. 171:1017-1027(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Sequence of a 1.4 kb Eco RI fragment of Azotobacter vinelandii nif DNA."
      Hiratsuka K., Roy K.L.
      Nucleic Acids Res. 16:1207-1207(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-409.
      Strain: ATCC 13705 / OP1 / DSM 366 / NCIB 11614 / LMG 3878 / UW.
    3. "Complete nucleotide sequence of the Azotobacter vinelandii nitrogenase structural gene cluster."
      Brigle K.E., Newton W.E., Dean D.R.
      Gene 37:37-44(1985) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    4. "Isolation and partial characterization of two different subunits from the molybdenum-iron protein of Azotobacter vinelandii nitrogenase."
      Lundell D.J., Howard J.B.
      J. Biol. Chem. 253:3422-3426(1978) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-20.
    5. "Crystallographic structure and functional implications of the nitrogenase molybdenum-iron protein from Azotobacter vinelandii."
      Kim J., Rees D.C.
      Nature 360:553-560(1992)
      Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS).
    6. "Structure of ADP x [AlF(4)](-)-stabilized nitrogenase complex and its implications for signal transduction."
      Schindelin H., Kisker C., Schlessman J.L., Howard J.B., Rees D.C.
      Nature 387:370-376(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) IN COMPLEX WITH FE(8)-S(7) CLUSTER AND IRON-SULFUR-MOLYBDENUM CLUSTER, SUBUNIT, COFACTOR.
    7. "Redox-dependent structural changes in the nitrogenase P-cluster."
      Peters J.W., Stowell M.H.B., Soltis S.M., Finnegan M.G., Johnson M.K., Rees D.C.
      Biochemistry 36:1181-1187(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH FE(8)-S(7) CLUSTER AND IRON-SULFUR-MOLYBDENUM CLUSTER, SUBUNIT, COFACTOR.
    8. "MgATP-bound and nucleotide-free structures of a nitrogenase protein complex between the Leu 127Delta-Fe-protein and the MoFe-protein."
      Chiu H.-J., Peters J.W., Lanzilotta W.N., Ryle M.J., Seefeldt L.C., Howard J.B., Rees D.C.
      Biochemistry 40:641-650(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) IN COMPLEX WITH FE(8)-S(7) CLUSTER AND IRON-SULFUR-MOLYBDENUM CLUSTER, SUBUNIT, COFACTOR.
    9. "Mechanistic features and structure of the nitrogenase alpha-Gln195 MoFe protein."
      Soerlie M., Christiansen J., Lemon B.J., Peters J.W., Dean D.R., Hales B.J.
      Biochemistry 40:1540-1549(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF MUTANT GLN-195 IN COMPLEX WITH IRON-SULFUR-MOLYBDENUM CLUSTER, SUBUNIT, COFACTOR.
    10. "Biochemical and structural characterization of the cross-linked complex of nitrogenase: comparison to the ADP-AlF4(-)-stabilized structure."
      Schmid B., Einsle O., Chiu H.J., Willing A., Yoshida M., Howard J.B., Rees D.C.
      Biochemistry 41:15557-15565(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF CROSS-LINKED HETERODIMER WITH FE-PROTEIN IN COMPLEX WITH FE(8)-S(7) CLUSTER AND IRON-SULFUR-MOLYBDENUM CLUSTER, SUBUNIT, COFACTOR.
    11. Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
    12. "Nitrogenase MoFe-protein at 1.16 A resolution: a central ligand in the FeMo-cofactor."
      Einsle O., Tezcan F.A., Andrade S.L.A., Schmid B., Yoshida M., Howard J.B., Rees D.C.
      Science 297:1696-1700(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.16 ANGSTROMS) IN COMPLEX WITH FE(7)-MO-S(9)-N CLUSTER, SUBUNIT, COFACTOR.
    13. "Nitrogenase complexes: multiple docking sites for a nucleotide switch protein."
      Tezcan F.A., Kaiser J.T., Mustafi D., Walton M.Y., Howard J.B., Rees D.C.
      Science 309:1377-1380(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) IN COMPLEX WITH FE(7)-MO-S(9)-N CLUSTER AND FE(8)-S(7) CLUSTER, SUBUNIT, COFACTOR.
    14. "Evidence for interstitial carbon in nitrogenase FeMo cofactor."
      Spatzal T., Aksoyoglu M., Zhang L., Andrade S.L., Schleicher E., Weber S., Rees D.C., Einsle O.
      Science 334:940-940(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.00 ANGSTROMS) IN COMPLEX WITH FE(8)-S(7) CLUSTER AND 7FE-MO-9S-C-HOMOCITRYL CLUSTER, COFACTOR, SUBUNIT.

    Entry informationi

    Entry nameiNIFD_AZOVI
    AccessioniPrimary (citable) accession number: P07328
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 1, 1988
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 101 of the entry and version 3 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