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Protein

Nitrogenase molybdenum-iron protein alpha chain

Gene

nifD

Organism
Klebsiella pneumoniae
Status
Reviewed-Annotation score: Annotation score: 4 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:

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi63Iron-sulfur (8Fe-7S); shared with beta chain1
Metal bindingi89Iron-sulfur (8Fe-7S); shared with beta chain1
Metal bindingi155Iron-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

Keywordsi

Molecular functionOxidoreductase
Biological processNitrogen fixation
LigandATP-binding, Iron, Iron-sulfur, Metal-binding, Molybdenum, Nucleotide-binding

Enzyme and pathway databases

BioCyciMetaCyc:NIFDKLEB-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:nifD
OrganismiKlebsiella pneumoniae
Taxonomic identifieri573 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeKlebsiella

Subcellular locationi

GO - Cellular componenti

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001530691 – 483Nitrogenase molybdenum-iron protein alpha chainAdd BLAST483

Interactioni

Subunit structurei

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

Protein-protein interaction databases

DIPiDIP-6206N.

Structurei

Secondary structure

1483
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi5 – 18Combined sources14
Helixi23 – 29Combined sources7
Helixi30 – 32Combined sources3
Beta strandi33 – 35Combined sources3
Helixi44 – 46Combined sources3
Helixi64 – 68Combined sources5
Helixi69 – 73Combined sources5
Beta strandi79 – 87Combined sources9
Helixi88 – 92Combined sources5
Turni93 – 95Combined sources3
Turni105 – 107Combined sources3
Helixi121 – 126Combined sources6
Helixi129 – 142Combined sources14
Beta strandi147 – 153Combined sources7
Helixi156 – 159Combined sources4
Helixi164 – 175Combined sources12
Beta strandi179 – 182Combined sources4
Beta strandi188 – 191Combined sources4
Helixi192 – 206Combined sources15
Turni207 – 213Combined 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
Helixi301 – 313Combined sources13
Helixi318 – 346Combined sources29
Beta strandi350 – 358Combined sources9
Helixi359 – 362Combined sources4
Helixi364 – 369Combined sources6
Beta strandi373 – 381Combined sources9
Helixi384 – 390Combined sources7
Helixi391 – 393Combined sources3
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

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1H1LX-ray1.90A/C3-483[»]
1QGUX-ray1.60A/C3-480[»]
1QH1X-ray1.60A/C3-480[»]
1QH8X-ray1.60A/C3-480[»]
ProteinModelPortaliP00466.
SMRiP00466.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP00466.

Family & Domainsi

Sequence similaritiesi

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

Family and domain databases

CDDicd01976. Nitrogenase_MoFe_alpha. 1 hit.
InterProiView protein in InterPro
IPR000510. Nase/OxRdtase_comp1.
IPR010143. Nase_comp1_asu.
IPR000318. Nase_comp1_CS.
IPR005972. Nase_Mo-Fe_asu.
PfamiView protein in Pfam
PF00148. Oxidored_nitro. 1 hit.
TIGRFAMsiTIGR01862. N2-ase-Ialpha. 1 hit.
TIGR01282. nifD. 1 hit.
PROSITEiView protein in PROSITE
PS00699. NITROGENASE_1_1. 1 hit.
PS00090. NITROGENASE_1_2. 1 hit.

Sequencei

Sequence statusi: Complete.

P00466-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MMTNATGERN LALIQEVLEV FPETARKERR KHMMVSDPKM KSVGKCIISN
60 70 80 90 100
RKSQPGVMTV RGCAYAGSKG VVFGPIKDMA HISHGPAGCG QYSRAERRNY
110 120 130 140 150
YTGVSGVDSF GTLNFTSDFQ ERDIVFGGDK KLSKLIEEME LLFPLTKGIT
160 170 180 190 200
IQSECPVGLI GDDISAVANA SSKALDKPVI PVRCEGFRGV SQSLGHHIAN
210 220 230 240 250
DVVRDWILNN REGQPFETTP YDVAIIGDYN IGGDAWASRI LLEEMGLRVV
260 270 280 290 300
AQWSGDGTLV EMENTPFVKL NLVHCYRSMN YIARHMEEKH QIPWMEYNFF
310 320 330 340 350
GPTKIAESLR KIADQFDDTI RANAEAVIAR YEGQMAAIIA KYRPRLEGRK
360 370 380 390 400
VLLYMGGLRP RHVIGAYEDL GMEIIAAGYE FAHNDDYDRT LPDLKEGTLL
410 420 430 440 450
FDDASSYELE AFVKALKPDL IGSGIKEKYI FQKMGVPFRQ MHSWDYSGPY
460 470 480
HGYDGFAIFA RDMDMTLNNP AWNELTAPWL KSA
Length:483
Mass (Da):54,158
Last modified:July 1, 1989 - v2
Checksum:i4A2BA83B2C0C6EE7
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti16E → Q (PubMed:3322262).Curated1
Sequence conflicti261 – 264EMEN → GDGD in CAA31179 (PubMed:3211766).Curated4
Sequence conflicti288E → D in CAA31179 (PubMed:3211766).Curated1
Sequence conflicti341 – 343KYR → NIA in CAA31179 (PubMed:3211766).Curated3
Sequence conflicti349 – 361RKVLL…GLRPR → LRCCSIWRLP in CAA31179 (PubMed:3211766).CuratedAdd BLAST13
Sequence conflicti355M → I in CAA31667 (Ref. 2) Curated1
Sequence conflicti469N → T in CAA31179 (PubMed:3211766).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y00316 Genomic DNA. Translation: CAA68413.1.
X07748 Genomic DNA. Translation: CAA30571.1.
X13303 Genomic DNA. Translation: CAA31667.1.
V00631 Genomic DNA. Translation: CAA23904.1.
X12649 Genomic DNA. Translation: CAA31179.1.
X06243 Genomic DNA. Translation: CAA29587.1.
PIRiS01729. NIKBMA.

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.

Entry informationi

Entry nameiNIFD_KLEPN
AccessioniPrimary (citable) accession number: P00466
Secondary accession number(s): P09770
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 1, 1989
Last modified: November 2, 2016
This is version 106 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Caution

The authors of PubMed:3211766 originally stated that their sequence was from Frankia sp.Curated

Keywords - Technical termi

3D-structure

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families