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Protein

Nitrogenase molybdenum-iron protein alpha chain

Gene

nifD1

more
Organism
Rhizobium sp. (strain NGR234)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Protein inferred from homologyi

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

Protein has several cofactor binding sites:

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

GO - Biological processi

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

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 Componenti: Plasmid sym pNGR234a

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

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).

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.
OMAiSTCPVGL.
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

« Hide

        10         20         30         40         50
MSLDYENDSA LHQELITQVL SQYPHKAAKR RQKHLSVASD REAVGEEGET
60 70 80 90 100
LSECDVKSNI KSIPGVMTIR GCAYAGSKGV VWGPVKDMVH ISHGPVGCGQ
110 120 130 140 150
YSWSQRRNYY VGTTGVDTFV TMQFTSDFQE KDIVFGGDKK LEQVIDEIEE
160 170 180 190 200
LFPLNNGITI QSECPIGLIG DDIEAVSRKK AAEHETTIVP VRCEGFRGVS
210 220 230 240 250
QSLGHHIAND AIRDWVFDKA DGKTDVEFET GPYDVNVIGD YNIGGDAWAS
260 270 280 290 300
RILLEEIGLR VVGNWSGDAT LAEVERAPRA KLNLIHCYRS MNYICRHMEE
310 320 330 340 350
RYAIPWMEYN FFGPSQIEAS LRKIARHFGP TIEERAERVI AKYRPLVDAV
360 370 380 390 400
IDKYWPRLQG KRVMLYVGGL RPRHVITAYE DLGMQIVGTG YEFAHNDDYQ
410 420 430 440 450
RTGHYVKTGT LIYDDATSYE LDTFIERIRP DLVGSGIKEK YPVQKMGIPF
460 470 480 490 500
RQMHSWDYSG PYHGYDGFAI FARDMDLAIN NPVWDLYDAP WKKMTVPTAA

VAAE
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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

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

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Phylogenomic databases

eggNOGiCOG2710.
HOGENOMiHOG000005528.
KOiK02586.
OMAiSTCPVGL.
OrthoDBiEOG6VHZ72.

Enzyme and pathway databases

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

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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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: June 24, 2015
This is version 103 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.