NIR_ARATH
ID NIR_ARATH Reviewed; 586 AA.
AC Q39161; Q8H163; Q8H164;
DT 11-OCT-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 153.
DE RecName: Full=Ferredoxin--nitrite reductase, chloroplastic;
DE Short=NiR;
DE EC=1.7.7.1;
DE Flags: Precursor;
GN Name=NIR1; Synonyms=NIR; OrderedLocusNames=At2g15620; ORFNames=F9O13.17;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=7894060; DOI=10.3109/10425179409039705;
RA Tanaka T., Ida S., Irifune K., Oeda K., Morikawa H.;
RT "Nucleotide sequence of a gene for nitrite reductase from Arabidopsis
RT thaliana.";
RL DNA Seq. 5:57-61(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=cv. C24; TISSUE=Leaf;
RA Hara K., Komaba S., Takahashi M., Goshima N., Morikawa H.;
RL Submitted (JUL-1997) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(1999).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [6]
RP CHARACTERIZATION, AND INDUCTION.
RX PubMed=9161026; DOI=10.1046/j.1365-313x.1997.11040625.x;
RA Crete P., Caboche M., Meyer C.;
RT "Nitrite reductase expression is regulated at the post-transcriptional
RT level by the nitrogen source in Nicotiana plumbaginifolia and Arabidopsis
RT thaliana.";
RL Plant J. 11:625-634(1997).
RN [7]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=11402201; DOI=10.1104/pp.126.2.731;
RA Takahashi M., Sasaki Y., Ida S., Morikawa H.;
RT "Nitrite reductase gene enrichment improves assimilation of NO(2) in
RT Arabidopsis.";
RL Plant Physiol. 126:731-741(2001).
RN [8]
RP UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-103, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=cv. Landsberg erecta;
RX PubMed=17272265; DOI=10.1074/mcp.m600408-mcp200;
RA Maor R., Jones A., Nuehse T.S., Studholme D.J., Peck S.C., Shirasu K.;
RT "Multidimensional protein identification technology (MudPIT) analysis of
RT ubiquitinated proteins in plants.";
RL Mol. Cell. Proteomics 6:601-610(2007).
CC -!- FUNCTION: Catalyzes the six-electron reduction of nitrite to ammonium.
CC {ECO:0000269|PubMed:11402201}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 H2O + NH4(+) + 6 oxidized [2Fe-2S]-[ferredoxin] = 8 H(+) +
CC nitrite + 6 reduced [2Fe-2S]-[ferredoxin]; Xref=Rhea:RHEA:18041,
CC Rhea:RHEA-COMP:10000, Rhea:RHEA-COMP:10001, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16301, ChEBI:CHEBI:28938,
CC ChEBI:CHEBI:33737, ChEBI:CHEBI:33738; EC=1.7.7.1;
CC -!- COFACTOR:
CC Name=siroheme; Xref=ChEBI:CHEBI:60052;
CC Note=Binds 1 siroheme per subunit.;
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Note=Binds 1 [4Fe-4S] cluster per subunit.;
CC -!- PATHWAY: Nitrogen metabolism; nitrate reduction (assimilation).
CC -!- SUBUNIT: Monomer.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:11402201}.
CC -!- INDUCTION: By nitrate and by light. {ECO:0000269|PubMed:9161026}.
CC -!- SIMILARITY: Belongs to the nitrite and sulfite reductase 4Fe-4S domain
CC family. {ECO:0000305}.
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DR EMBL; D14824; BAA03561.1; -; Genomic_DNA.
DR EMBL; AB006032; BAA21672.1; -; mRNA.
DR EMBL; AC006248; AAD17406.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC06424.1; -; Genomic_DNA.
DR EMBL; AF360320; AAK26030.1; -; mRNA.
DR EMBL; AY045608; AAK73966.1; -; mRNA.
DR EMBL; AY093995; AAM16256.1; -; mRNA.
DR EMBL; AY142685; AAN13223.1; -; mRNA.
DR EMBL; BT000685; AAN31830.1; -; mRNA.
DR EMBL; BT000686; AAN31831.1; -; mRNA.
DR PIR; C84531; C84531.
DR RefSeq; NP_179164.1; NM_127123.3.
DR AlphaFoldDB; Q39161; -.
DR SMR; Q39161; -.
DR BioGRID; 1414; 6.
DR IntAct; Q39161; 2.
DR STRING; 3702.AT2G15620.1; -.
DR iPTMnet; Q39161; -.
DR MetOSite; Q39161; -.
DR PaxDb; Q39161; -.
DR PRIDE; Q39161; -.
DR ProteomicsDB; 236829; -.
DR EnsemblPlants; AT2G15620.1; AT2G15620.1; AT2G15620.
DR GeneID; 816055; -.
DR Gramene; AT2G15620.1; AT2G15620.1; AT2G15620.
DR KEGG; ath:AT2G15620; -.
DR Araport; AT2G15620; -.
DR TAIR; locus:2053654; AT2G15620.
DR eggNOG; KOG0560; Eukaryota.
DR HOGENOM; CLU_015667_2_2_1; -.
DR InParanoid; Q39161; -.
DR OMA; IKISGCM; -.
DR OrthoDB; 333458at2759; -.
DR PhylomeDB; Q39161; -.
DR UniPathway; UPA00653; -.
DR PRO; PR:Q39161; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q39161; baseline and differential.
DR Genevisible; Q39161; AT.
DR GO; GO:0048046; C:apoplast; HDA:TAIR.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0005739; C:mitochondrion; HDA:TAIR.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0048307; F:ferredoxin-nitrite reductase activity; IEA:UniProtKB-EC.
DR GO; GO:0020037; F:heme binding; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0050421; F:nitrite reductase (NO-forming) activity; ISS:TAIR.
DR GO; GO:0042128; P:nitrate assimilation; IEA:UniProtKB-UniPathway.
DR GO; GO:0010167; P:response to nitrate; IEP:TAIR.
DR Gene3D; 3.30.413.10; -; 2.
DR InterPro; IPR005117; NiRdtase/SiRdtase_haem-b_fer.
DR InterPro; IPR036136; Nit/Sulf_reduc_fer-like_dom_sf.
DR InterPro; IPR006067; NO2/SO3_Rdtase_4Fe4S_dom.
DR InterPro; IPR045854; NO2/SO3_Rdtase_4Fe4S_sf.
DR InterPro; IPR006066; NO2/SO3_Rdtase_FeS/sirohaem_BS.
DR Pfam; PF01077; NIR_SIR; 2.
DR Pfam; PF03460; NIR_SIR_ferr; 2.
DR PRINTS; PR00397; SIROHAEM.
DR SUPFAM; SSF55124; SSF55124; 2.
DR SUPFAM; SSF56014; SSF56014; 2.
DR PROSITE; PS00365; NIR_SIR; 1.
PE 1: Evidence at protein level;
KW 4Fe-4S; Chloroplast; Electron transport; Heme; Iron; Iron-sulfur;
KW Isopeptide bond; Metal-binding; Nitrate assimilation; Oxidoreductase;
KW Plastid; Reference proteome; Repeat; Transit peptide; Transport;
KW Ubl conjugation.
FT TRANSIT 1..25
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 26..586
FT /note="Ferredoxin--nitrite reductase, chloroplastic"
FT /id="PRO_0000019703"
FT REGION 1..20
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 464
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 470
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 505
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 509
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 509
FT /ligand="siroheme"
FT /ligand_id="ChEBI:CHEBI:60052"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000250"
FT CROSSLNK 103
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0007744|PubMed:17272265"
FT CONFLICT 77
FT /note="R -> G (in Ref. 5; AAN31831)"
FT /evidence="ECO:0000305"
FT CONFLICT 214
FT /note="P -> Q (in Ref. 5; AAN31830)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 586 AA; 65505 MW; 6AACF1FE9FF7E1F2 CRC64;
MTSFSLTFTS PLLPSSSTKP KRSVLVAAAQ TTAPAESTAS VDADRLEPRV ELKDGFFILK
EKFRKGINPQ EKVKIEREPM KLFMENGIEE LAKKSMEELD SEKSSKDDID VRLKWLGLFH
RRKHQYGKFM MRLKLPNGVT TSAQTRYLAS VIRKYGEDGC ADVTTRQNWQ IRGVVLPDVP
EILKGLASVG LTSLQSGMDN VRNPVGNPIA GIDPEEIVDT RPYTNLLSQF ITANSQGNPD
FTNLPRKWNV CVVGTHDLYE HPHINDLAYM PANKDGRFGF NLLVGGFFSP KRCEEAIPLD
AWVPADDVLP LCKAVLEAYR DLGTRGNRQK TRMMWLIDEL GVEGFRTEVE KRMPNGKLER
GSSEDLVNKQ WERRDYFGVN PQKQEGLSFV GLHVPVGRLQ ADDMDELARL ADTYGSGELR
LTVEQNIIIP NVETSKTEAL LQEPFLKNRF SPEPSILMKG LVACTGSQFC GQAIIETKLR
ALKVTEEVER LVSVPRPIRM HWTGCPNTCG QVQVADIGFM GCLTRGEEGK PVEGADVYVG
GRIGSDSHIG EIYKKGVRVT ELVPLVAEIL IKEFGAVPRE REENED
