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P07328

- NIFD_AZOVI

UniProt

P07328 - NIFD_AZOVI

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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

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.8 Publications
Binds 1 7Fe-Mo-9S-C-homocitryl cluster per subunit.8 Publications

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
Complete GO annotation...

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
Complete GO annotation...

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.

Miscellaneous databases

EvolutionaryTraceiP07328.

Family & Domainsi

Sequence similaritiesi

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

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti3 – 31G → R in AAA22143. 1 Publication
Sequence conflicti190 – 1901S → C in AAA22143. 1 Publication
Sequence conflicti212 – 2121E → A in AAA22143. 1 Publication
Sequence conflicti258 – 2614SISE → YISQ1 Publication
Sequence conflicti407 – 4071Y → M in AAA22143. 1 Publication
Sequence conflicti440 – 4401E → Q1 Publication
Sequence conflicti440 – 4401E → Q1 Publication

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: July 9, 2014
This is version 100 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

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