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P07328 (NIFD_AZOVI) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 99. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Nitrogenase molybdenum-iron protein alpha chain

EC=1.18.6.1
Alternative name(s):
Dinitrogenase
Nitrogenase component I
Gene names
Name:nifD
OrganismAzotobacter vinelandii
Taxonomic identifier354 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaeAzotobacter

Protein attributes

Sequence length492 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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

Catalytic activity

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

Cofactor

Binds 1 8Fe-7S cluster per heterodimer. Ref.6 Ref.7 Ref.8 Ref.9 Ref.10 Ref.12 Ref.13 Ref.14

Binds 1 7Fe-Mo-9S-C-homocitryl cluster per subunit. Ref.6 Ref.7 Ref.8 Ref.9 Ref.10 Ref.12 Ref.13 Ref.14

Subunit structure

Tetramer of two alpha and two beta chains. Forms complex with the iron protein (nitrogenase component 2). Ref.6 Ref.7 Ref.8 Ref.9 Ref.10 Ref.12 Ref.13 Ref.14

Sequence similarities

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.4
Chain2 – 492491Nitrogenase molybdenum-iron protein alpha chain
PRO_0000153058

Sites

Metal binding621Iron-sulfur (8Fe-7S); shared with beta chain
Metal binding881Iron-sulfur (8Fe-7S); shared with beta chain
Metal binding1541Iron-sulfur (8Fe-7S); shared with beta chain
Metal binding2751Molybdenum-iron-sulfur-carbon (7Fe-Mo-9S-C-homocitryl)
Metal binding4421Molybdenum-iron-sulfur-carbon (7Fe-Mo-9S-C-homocitryl); via pros nitrogen

Experimental info

Mutagenesis1951H → Q: No nitrogenase activity.
Sequence conflict31G → R in AAA22143. Ref.3
Sequence conflict1901S → C in AAA22143. Ref.3
Sequence conflict2121E → A in AAA22143. Ref.3
Sequence conflict258 – 2614SISE → YISQ Ref.3
Sequence conflict4071Y → M in AAA22143. Ref.3
Sequence conflict4401E → Q Ref.1
Sequence conflict4401E → Q Ref.3

Secondary structure

..................................................................................... 492
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P07328 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: 7D4B2CF5E99664D7

FASTA49255,289
        10         20         30         40         50         60 
MTGMSREEVE SLIQEVLEVY PEKARKDRNK HLAVNDPAVT QSKKCIISNK KSQPGLMTIR 

        70         80         90        100        110        120 
GCAYAGSKGV VWGPIKDMIH ISHGPVGCGQ YSRAGRRNYY IGTTGVNAFV TMNFTSDFQE 

       130        140        150        160        170        180 
KDIVFGGDKK LAKLIDEVET LFPLNKGISV QSECPIGLIG DDIESVSKVK GAELSKTIVP 

       190        200        210        220        230        240 
VRCEGFRGVS QSLGHHIAND AVRDWVLGKR DEDTTFASTP YDVAIIGDYN IGGDAWSSRI 

       250        260        270        280        290        300 
LLEEMGLRCV AQWSGDGSIS EIELTPKVKL NLVHCYRSMN YISRHMEEKY GIPWMEYNFF 

       310        320        330        340        350        360 
GPTKTIESLR AIAAKFDESI QKKCEEVIAK YKPEWEAVVA KYRPRLEGKR VMLYIGGLRP 

       370        380        390        400        410        420 
RHVIGAYEDL GMEVVGTGYE FAHNDDYDRT MKEMGDSTLL YDDVTGYEFE EFVKRIKPDL 

       430        440        450        460        470        480 
IGSGIKEKFI FQKMGIPFRE MHSWDYSGPY HGFDGFAIFA RDMDMTLNNP CWKKLQAPWE 

       490 
ASEGAEKVAA SA 

« Hide

References

[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]"Structure of a cofactor-deficient nitrogenase MoFe protein."
Schmid B., Ribbe M.W., Einsle O., Yoshida M., Thomas L.M., Dean D.R., Rees D.C., Burgess B.K.
Science 296:352-356(2002) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M20568 Genomic DNA. Translation: AAA64710.1.
M11579 Genomic DNA. Translation: AAA22143.1.
X06886 Genomic DNA. Translation: CAA30004.1.
PIRNIAVMA. A43049.

3D structure databases

PDBe
RCSB PDB
PDBj
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/C2-491[»]
2AFIX-ray3.10A/C/I/K2-491[»]
2AFKX-ray2.30A/C2-491[»]
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[»]
ProteinModelPortalP07328.
SMRP07328. Positions 4-481.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-6252N.
MINTMINT-1508543.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Enzyme and pathway databases

BioCycMetaCyc:MONOMER-16520.

Family and domain databases

InterProIPR000510. Nase/OxRdtase_comp1.
IPR010143. Nase_comp1_asu.
IPR000318. Nase_comp1_CS.
IPR005972. Nase_Mo-Fe_asu.
[Graphical view]
PfamPF00148. Oxidored_nitro. 1 hit.
[Graphical view]
TIGRFAMsTIGR01862. N2-ase-Ialpha. 1 hit.
TIGR01282. nifD. 1 hit.
PROSITEPS00699. NITROGENASE_1_1. 1 hit.
PS00090. NITROGENASE_1_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP07328.

Entry information

Entry nameNIFD_AZOVI
AccessionPrimary (citable) accession number: P07328
Entry history
Integrated into UniProtKB/Swiss-Prot: April 1, 1988
Last sequence update: January 23, 2007
Last modified: March 19, 2014
This is version 99 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references