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Protein

Ferredoxin--nitrite reductase, chloroplastic

Gene

NIR1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the six-electron reduction of nitrite to ammonium.1 Publication

Catalytic activityi

NH3 + 2 H2O + 6 oxidized ferredoxin = nitrite + 6 reduced ferredoxin + 7 H+.

Cofactori

Protein has several cofactor binding sites:

Pathwayi: nitrate reduction (assimilation)

This protein is involved in the pathway nitrate reduction (assimilation), which is part of Nitrogen metabolism.
View all proteins of this organism that are known to be involved in the pathway nitrate reduction (assimilation) and in Nitrogen metabolism.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi464 – 4641Iron-sulfur (4Fe-4S)By similarity
Metal bindingi470 – 4701Iron-sulfur (4Fe-4S)By similarity
Metal bindingi505 – 5051Iron-sulfur (4Fe-4S)By similarity
Metal bindingi509 – 5091Iron (siroheme axial ligand)By similarity
Metal bindingi509 – 5091Iron-sulfur (4Fe-4S)By similarity

GO - Molecular functioni

GO - Biological processi

  • nitrate assimilation Source: UniProtKB-UniPathway
  • response to nitrate Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Electron transport, Nitrate assimilation, Transport

Keywords - Ligandi

4Fe-4S, Heme, Iron, Iron-sulfur, Metal-binding

Enzyme and pathway databases

UniPathwayiUPA00653.

Names & Taxonomyi

Protein namesi
Recommended name:
Ferredoxin--nitrite reductase, chloroplastic (EC:1.7.7.1)
Short name:
NiR
Gene namesi
Name:NIR1
Synonyms:NIR
Ordered Locus Names:At2g15620
ORF Names:F9O13.17
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 2

Organism-specific databases

TAIRiAT2G15620.

Subcellular locationi

GO - Cellular componenti

  • apoplast Source: TAIR
  • chloroplast Source: TAIR
  • chloroplast stroma Source: TAIR
  • membrane Source: TAIR
  • mitochondrion Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Plastid

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 2525ChloroplastSequence analysisAdd
BLAST
Chaini26 – 586561Ferredoxin--nitrite reductase, chloroplasticPRO_0000019703Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Cross-linki103 – 103Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

PaxDbiQ39161.
PRIDEiQ39161.

PTM databases

iPTMnetiQ39161.

Expressioni

Inductioni

By nitrate and by light.1 Publication

Gene expression databases

GenevisibleiQ39161. AT.

Interactioni

Subunit structurei

Monomer.

Protein-protein interaction databases

BioGridi1414. 3 interactions.
IntActiQ39161. 2 interactions.
MINTiMINT-8059587.
STRINGi3702.AT2G15620.1.

Structurei

3D structure databases

ProteinModelPortaliQ39161.
SMRiQ39161. Positions 41-579.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Repeat, Transit peptide

Phylogenomic databases

eggNOGiKOG0560. Eukaryota.
COG0155. LUCA.
HOGENOMiHOG000249408.
InParanoidiQ39161.
KOiK00366.
OMAiVQSGMDN.
PhylomeDBiQ39161.

Family and domain databases

Gene3Di3.90.480.10. 2 hits.
InterProiIPR005117. NiRdtase/SiRdtase_haem-b_fer.
IPR006067. NO2/SO3_Rdtase_4Fe4S_dom.
IPR006066. NO2/SO3_Rdtase_FeS/sirohaem_BS.
[Graphical view]
PfamiPF01077. NIR_SIR. 2 hits.
PF03460. NIR_SIR_ferr. 2 hits.
[Graphical view]
PRINTSiPR00397. SIROHAEM.
SUPFAMiSSF55124. SSF55124. 2 hits.
PROSITEiPS00365. NIR_SIR. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q39161-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTSFSLTFTS PLLPSSSTKP KRSVLVAAAQ TTAPAESTAS VDADRLEPRV
60 70 80 90 100
ELKDGFFILK EKFRKGINPQ EKVKIEREPM KLFMENGIEE LAKKSMEELD
110 120 130 140 150
SEKSSKDDID VRLKWLGLFH RRKHQYGKFM MRLKLPNGVT TSAQTRYLAS
160 170 180 190 200
VIRKYGEDGC ADVTTRQNWQ IRGVVLPDVP EILKGLASVG LTSLQSGMDN
210 220 230 240 250
VRNPVGNPIA GIDPEEIVDT RPYTNLLSQF ITANSQGNPD FTNLPRKWNV
260 270 280 290 300
CVVGTHDLYE HPHINDLAYM PANKDGRFGF NLLVGGFFSP KRCEEAIPLD
310 320 330 340 350
AWVPADDVLP LCKAVLEAYR DLGTRGNRQK TRMMWLIDEL GVEGFRTEVE
360 370 380 390 400
KRMPNGKLER GSSEDLVNKQ WERRDYFGVN PQKQEGLSFV GLHVPVGRLQ
410 420 430 440 450
ADDMDELARL ADTYGSGELR LTVEQNIIIP NVETSKTEAL LQEPFLKNRF
460 470 480 490 500
SPEPSILMKG LVACTGSQFC GQAIIETKLR ALKVTEEVER LVSVPRPIRM
510 520 530 540 550
HWTGCPNTCG QVQVADIGFM GCLTRGEEGK PVEGADVYVG GRIGSDSHIG
560 570 580
EIYKKGVRVT ELVPLVAEIL IKEFGAVPRE REENED
Length:586
Mass (Da):65,505
Last modified:November 1, 1996 - v1
Checksum:i6AACF1FE9FF7E1F2
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti77 – 771R → G in AAN31831 (PubMed:14593172).Curated
Sequence conflicti214 – 2141P → Q in AAN31830 (PubMed:14593172).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D14824 Genomic DNA. Translation: BAA03561.1.
AB006032 mRNA. Translation: BAA21672.1.
AC006248 Genomic DNA. Translation: AAD17406.1.
CP002685 Genomic DNA. Translation: AEC06424.1.
AF360320 mRNA. Translation: AAK26030.1.
AY045608 mRNA. Translation: AAK73966.1.
AY093995 mRNA. Translation: AAM16256.1.
AY142685 mRNA. Translation: AAN13223.1.
BT000685 mRNA. Translation: AAN31830.1.
BT000686 mRNA. Translation: AAN31831.1.
PIRiC84531.
RefSeqiNP_179164.1. NM_127123.2.
UniGeneiAt.21870.

Genome annotation databases

EnsemblPlantsiAT2G15620.1; AT2G15620.1; AT2G15620.
GeneIDi816055.
GrameneiAT2G15620.1; AT2G15620.1; AT2G15620.
KEGGiath:AT2G15620.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D14824 Genomic DNA. Translation: BAA03561.1.
AB006032 mRNA. Translation: BAA21672.1.
AC006248 Genomic DNA. Translation: AAD17406.1.
CP002685 Genomic DNA. Translation: AEC06424.1.
AF360320 mRNA. Translation: AAK26030.1.
AY045608 mRNA. Translation: AAK73966.1.
AY093995 mRNA. Translation: AAM16256.1.
AY142685 mRNA. Translation: AAN13223.1.
BT000685 mRNA. Translation: AAN31830.1.
BT000686 mRNA. Translation: AAN31831.1.
PIRiC84531.
RefSeqiNP_179164.1. NM_127123.2.
UniGeneiAt.21870.

3D structure databases

ProteinModelPortaliQ39161.
SMRiQ39161. Positions 41-579.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi1414. 3 interactions.
IntActiQ39161. 2 interactions.
MINTiMINT-8059587.
STRINGi3702.AT2G15620.1.

PTM databases

iPTMnetiQ39161.

Proteomic databases

PaxDbiQ39161.
PRIDEiQ39161.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT2G15620.1; AT2G15620.1; AT2G15620.
GeneIDi816055.
GrameneiAT2G15620.1; AT2G15620.1; AT2G15620.
KEGGiath:AT2G15620.

Organism-specific databases

TAIRiAT2G15620.

Phylogenomic databases

eggNOGiKOG0560. Eukaryota.
COG0155. LUCA.
HOGENOMiHOG000249408.
InParanoidiQ39161.
KOiK00366.
OMAiVQSGMDN.
PhylomeDBiQ39161.

Enzyme and pathway databases

UniPathwayiUPA00653.

Miscellaneous databases

PROiQ39161.

Gene expression databases

GenevisibleiQ39161. AT.

Family and domain databases

Gene3Di3.90.480.10. 2 hits.
InterProiIPR005117. NiRdtase/SiRdtase_haem-b_fer.
IPR006067. NO2/SO3_Rdtase_4Fe4S_dom.
IPR006066. NO2/SO3_Rdtase_FeS/sirohaem_BS.
[Graphical view]
PfamiPF01077. NIR_SIR. 2 hits.
PF03460. NIR_SIR_ferr. 2 hits.
[Graphical view]
PRINTSiPR00397. SIROHAEM.
SUPFAMiSSF55124. SSF55124. 2 hits.
PROSITEiPS00365. NIR_SIR. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Nucleotide sequence of a gene for nitrite reductase from Arabidopsis thaliana."
    Tanaka T., Ida S., Irifune K., Oeda K., Morikawa H.
    DNA Seq. 5:57-61(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: cv. Columbia.
  2. Hara K., Komaba S., Takahashi M., Goshima N., Morikawa H.
    Submitted (JUL-1997) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: cv. C24.
    Tissue: Leaf.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  4. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  5. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  6. "Nitrite reductase expression is regulated at the post-transcriptional level by the nitrogen source in Nicotiana plumbaginifolia and Arabidopsis thaliana."
    Crete P., Caboche M., Meyer C.
    Plant J. 11:625-634(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION, INDUCTION.
  7. "Nitrite reductase gene enrichment improves assimilation of NO(2) in Arabidopsis."
    Takahashi M., Sasaki Y., Ida S., Morikawa H.
    Plant Physiol. 126:731-741(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION.
  8. "Multidimensional protein identification technology (MudPIT) analysis of ubiquitinated proteins in plants."
    Maor R., Jones A., Nuehse T.S., Studholme D.J., Peck S.C., Shirasu K.
    Mol. Cell. Proteomics 6:601-610(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-103.
    Strain: cv. Landsberg erecta.

Entry informationi

Entry nameiNIR_ARATH
AccessioniPrimary (citable) accession number: Q39161
Secondary accession number(s): Q8H163, Q8H164
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 11, 2004
Last sequence update: November 1, 1996
Last modified: February 17, 2016
This is version 123 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. 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.