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Protein

Nitrogenase molybdenum-iron protein alpha chain

Gene

nifD

Organism
Azotobacter vinelandii
Status
Reviewed-Annotation score: 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

Protein has several cofactor binding sites:

Enzyme regulationi

Nitrogenase holoenzyme is subject to "conformational protection" by FeSII; under oxidizing conditions FeSII binds to the holoenzyme and reversibly protects it from oxidation (PubMed:7830548).1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi62Iron-sulfur (8Fe-7S); shared with beta chain1
Metal bindingi88Iron-sulfur (8Fe-7S); shared with beta chain1
Metal bindingi154Iron-sulfur (8Fe-7S); shared with beta chain1
Metal bindingi275Molybdenum-iron-sulfur-carbon (7Fe-Mo-9S-C-homocitryl)1
Metal bindingi442Molybdenum-iron-sulfur-carbon (7Fe-Mo-9S-C-homocitryl); via pros nitrogen1

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

BioCyciMetaCyc:MONOMER-19493.
BRENDAi1.18.6.1. 49.

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

Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi195H → Q: No nitrogenase activity. 1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00001530582 – 492Nitrogenase molybdenum-iron protein alpha chainAdd BLAST491

Expressioni

Inductioni

Constitutively expressed during log and stationary phase in sucrose-limited cultures, its levels decrease during stationary phase (at protein level).1 Publication

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.
STRINGi322710.Avin_01390.

Structurei

Secondary structure

1492
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi6 – 17Combined sources12
Helixi22 – 29Combined sources8
Beta strandi32 – 34Combined sources3
Helixi42 – 44Combined sources3
Helixi63 – 67Combined sources5
Helixi68 – 72Combined sources5
Beta strandi78 – 86Combined sources9
Helixi87 – 91Combined sources5
Turni92 – 94Combined sources3
Turni104 – 106Combined sources3
Beta strandi110 – 112Combined sources3
Helixi120 – 125Combined sources6
Helixi128 – 141Combined sources14
Beta strandi148 – 152Combined sources5
Helixi155 – 158Combined sources4
Helixi163 – 174Combined sources12
Beta strandi178 – 181Combined sources4
Beta strandi187 – 190Combined sources4
Helixi191 – 205Combined sources15
Turni206 – 212Combined sources7
Beta strandi222 – 228Combined sources7
Turni232 – 235Combined sources4
Helixi236 – 244Combined sources9
Beta strandi248 – 254Combined sources7
Helixi259 – 264Combined sources6
Helixi265 – 267Combined sources3
Beta strandi269 – 274Combined sources6
Helixi276 – 290Combined sources15
Beta strandi294 – 296Combined sources3
Helixi302 – 313Combined sources12
Helixi318 – 346Combined sources29
Beta strandi350 – 353Combined sources4
Beta strandi355 – 358Combined sources4
Helixi359 – 362Combined sources4
Helixi364 – 368Combined sources5
Turni369 – 371Combined sources3
Beta strandi373 – 381Combined sources9
Helixi384 – 391Combined sources8
Beta strandi399 – 403Combined sources5
Helixi406 – 416Combined sources11
Beta strandi419 – 423Combined sources5
Helixi425 – 433Combined sources9
Beta strandi438 – 443Combined sources6
Helixi444 – 446Combined sources3
Helixi452 – 467Combined sources16
Helixi470 – 473Combined sources4
Beta strandi475 – 477Combined sources3
Helixi478 – 480Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
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[»]
4TKUX-ray1.43A/C1-492[»]
4TKVX-ray1.50A/C1-492[»]
4WNAX-ray2.00A/C1-492[»]
4WZAX-ray1.90A/C4-480[»]
4WZBX-ray2.30A/C4-480[»]
4XPIX-ray1.97A/C3-492[»]
5BVGX-ray1.60A/C1-492[»]
5BVHX-ray1.53A/C1-492[»]
5CX1X-ray1.75A/C/E/G/I/K/M/O1-480[»]
ProteinModelPortaliP07328.
SMRiP07328.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP07328.

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105D0B. Bacteria.
COG2710. LUCA.

Family and domain databases

CDDicd01976. Nitrogenase_MoFe_alpha. 1 hit.
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

        10         20         30         40         50
MTGMSREEVE SLIQEVLEVY PEKARKDRNK HLAVNDPAVT QSKKCIISNK
60 70 80 90 100
KSQPGLMTIR GCAYAGSKGV VWGPIKDMIH ISHGPVGCGQ YSRAGRRNYY
110 120 130 140 150
IGTTGVNAFV TMNFTSDFQE KDIVFGGDKK LAKLIDEVET LFPLNKGISV
160 170 180 190 200
QSECPIGLIG DDIESVSKVK GAELSKTIVP VRCEGFRGVS QSLGHHIAND
210 220 230 240 250
AVRDWVLGKR DEDTTFASTP YDVAIIGDYN IGGDAWSSRI LLEEMGLRCV
260 270 280 290 300
AQWSGDGSIS EIELTPKVKL NLVHCYRSMN YISRHMEEKY GIPWMEYNFF
310 320 330 340 350
GPTKTIESLR AIAAKFDESI QKKCEEVIAK YKPEWEAVVA KYRPRLEGKR
360 370 380 390 400
VMLYIGGLRP RHVIGAYEDL GMEVVGTGYE FAHNDDYDRT MKEMGDSTLL
410 420 430 440 450
YDDVTGYEFE EFVKRIKPDL IGSGIKEKFI FQKMGIPFRE MHSWDYSGPY
460 470 480 490
HGFDGFAIFA RDMDMTLNNP CWKKLQAPWE ASEGAEKVAA SA
Length:492
Mass (Da):55,289
Last modified:January 23, 2007 - v3
Checksum:i7D4B2CF5E99664D7
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti3G → R in AAA22143 (PubMed:3863780).Curated1
Sequence conflicti190S → C in AAA22143 (PubMed:3863780).Curated1
Sequence conflicti212E → A in AAA22143 (PubMed:3863780).Curated1
Sequence conflicti258 – 261SISE → YISQ in AAA22143 (PubMed:3863780).Curated4
Sequence conflicti407Y → M in AAA22143 (PubMed:3863780).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
Links Updated
M20568 Genomic DNA. Translation: AAA64710.1.
M11579 Genomic DNA. Translation: AAA22143.1.
X06886 Genomic DNA. Translation: CAA30004.1.
PIRiA43049. NIAVMA.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
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[»]
4TKUX-ray1.43A/C1-492[»]
4TKVX-ray1.50A/C1-492[»]
4WNAX-ray2.00A/C1-492[»]
4WZAX-ray1.90A/C4-480[»]
4WZBX-ray2.30A/C4-480[»]
4XPIX-ray1.97A/C3-492[»]
5BVGX-ray1.60A/C1-492[»]
5BVHX-ray1.53A/C1-492[»]
5CX1X-ray1.75A/C/E/G/I/K/M/O1-480[»]
ProteinModelPortaliP07328.
SMRiP07328.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-6252N.
MINTiMINT-1508543.
STRINGi322710.Avin_01390.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiENOG4105D0B. Bacteria.
COG2710. LUCA.

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-19493.
BRENDAi1.18.6.1. 49.

Miscellaneous databases

EvolutionaryTraceiP07328.

Family and domain databases

CDDicd01976. Nitrogenase_MoFe_alpha. 1 hit.
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...

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: November 2, 2016
This is version 116 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

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 one 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.