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Protein

Ferredoxin--nitrite reductase, chloroplastic

Gene

NIR

Organism
Spinacia oleracea (Spinach)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

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

Cofactori

Protein has several cofactor binding sites:
  • sirohemeNote: Binds 1 siroheme per subunit.
  • [4Fe-4S] clusterBy similarityNote: Binds 1 [4Fe-4S] cluster per subunit.By similarity

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 bindingi473 – 4731Iron-sulfur (4Fe-4S)
Metal bindingi479 – 4791Iron-sulfur (4Fe-4S)
Metal bindingi514 – 5141Iron-sulfur (4Fe-4S)
Metal bindingi518 – 5181Iron (siroheme axial ligand)
Metal bindingi518 – 5181Iron-sulfur (4Fe-4S)

GO - Molecular functioni

GO - Biological processi

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

BRENDAi1.7.7.1. 5812.
UniPathwayiUPA00653.

Names & Taxonomyi

Protein namesi
Recommended name:
Ferredoxin--nitrite reductase, chloroplastic (EC:1.7.7.1)
Gene namesi
Name:NIR
OrganismiSpinacia oleracea (Spinach)
Taxonomic identifieri3562 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaeCaryophyllalesAmaranthaceaeChenopodioideaeAnserineaeSpinacia

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Plastid

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 3232ChloroplastAdd
BLAST
Chaini33 – 594562Ferredoxin--nitrite reductase, chloroplasticPRO_0000019706Add
BLAST

Expressioni

Inductioni

By nitrate.

Interactioni

Subunit structurei

Monomer.

Structurei

Secondary structure

1
594
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi58 – 625Combined sources
Beta strandi65 – 684Combined sources
Helixi70 – 723Combined sources
Helixi78 – 858Combined sources
Helixi90 – 934Combined sources
Helixi96 – 1005Combined sources
Helixi105 – 1084Combined sources
Helixi112 – 1198Combined sources
Helixi121 – 1255Combined sources
Beta strandi127 – 1293Combined sources
Helixi131 – 1344Combined sources
Beta strandi138 – 1414Combined sources
Helixi145 – 1473Combined sources
Beta strandi148 – 1503Combined sources
Helixi151 – 16212Combined sources
Helixi163 – 1675Combined sources
Beta strandi170 – 1723Combined sources
Beta strandi178 – 1836Combined sources
Helixi185 – 1873Combined sources
Helixi188 – 1969Combined sources
Turni197 – 1993Combined sources
Beta strandi206 – 2105Combined sources
Turni217 – 2215Combined sources
Helixi230 – 24011Combined sources
Turni241 – 2455Combined sources
Helixi248 – 2503Combined sources
Beta strandi259 – 2613Combined sources
Helixi271 – 2733Combined sources
Beta strandi274 – 29320Combined sources
Beta strandi306 – 3138Combined sources
Helixi314 – 3163Combined sources
Helixi317 – 33115Combined sources
Helixi337 – 3393Combined sources
Helixi342 – 3498Combined sources
Helixi351 – 3599Combined sources
Beta strandi386 – 3905Combined sources
Beta strandi396 – 4016Combined sources
Helixi404 – 4063Combined sources
Helixi410 – 42314Combined sources
Beta strandi424 – 4318Combined sources
Turni432 – 4343Combined sources
Beta strandi435 – 4428Combined sources
Turni443 – 4453Combined sources
Helixi446 – 4494Combined sources
Helixi453 – 4564Combined sources
Turni465 – 4684Combined sources
Beta strandi469 – 4724Combined sources
Helixi475 – 4773Combined sources
Helixi487 – 50014Combined sources
Beta strandi508 – 5147Combined sources
Helixi521 – 5233Combined sources
Beta strandi524 – 53411Combined sources
Beta strandi540 – 5489Combined sources
Beta strandi560 – 5678Combined sources
Turni568 – 5703Combined sources
Helixi571 – 58212Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2AKJX-ray2.80A33-594[»]
ProteinModelPortaliP05314.
SMRiP05314. Positions 54-588.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP05314.

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transit peptide

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.

P05314-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MASLPVNKII PSSTTLLSSS NNNRRRNNSS IRCQKAVSPA AETAAVSPSV
60 70 80 90 100
DAARLEPRVE ERDGFWVLKE EFRSGINPAE KVKIEKDPMK LFIEDGISDL
110 120 130 140 150
ATLSMEEVDK SKHNKDDIDV RLKWLGLFHR RKHHYGRFMM RLKLPNGVTT
160 170 180 190 200
SEQTRYLASV IKKYGKDGCA DVTTRQNWQI RGVVLPDVPE IIKGLESVGL
210 220 230 240 250
TSLQSGMDNV RNPVGNPLAG IDPHEIVDTR PFTNLISQFV TANSRGNLSI
260 270 280 290 300
TNLPRKWNPC VIGSHDLYEH PHINDLAYMP ATKNGKFGFN LLVGGFFSIK
310 320 330 340 350
RCEEAIPLDA WVSAEDVVPV CKAMLEAFRD LGFRGNRQKC RMMWLIDELG
360 370 380 390 400
MEAFRGEVEK RMPEQVLERA SSEELVQKDW ERREYLGVHP QKQQGLSFVG
410 420 430 440 450
LHIPVGRLQA DEMEELARIA DVYGSGELRL TVEQNIIIPN VENSKIDSLL
460 470 480 490 500
NEPLLKERYS PEPPILMKGL VACTGSQFCG QAIIETKARA LKVTEEVQRL
510 520 530 540 550
VSVTRPVRMH WTGCPNSCGQ VQVADIGFMG CMTRDENGKP CEGADVFVGG
560 570 580 590
RIGSDSHLGD IYKKAVPCKD LVPVVAEILI NQFGAVPRER EEAE
Length:594
Mass (Da):66,394
Last modified:November 1, 1988 - v1
Checksum:i2B3DCAAC16DE06A3
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti221 – 2211I → V Probable allelic variation.

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X07568 mRNA. Translation: CAA30453.1.
X17031 Genomic DNA. Translation: CAA34893.1.
PIRiS16603.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X07568 mRNA. Translation: CAA30453.1.
X17031 Genomic DNA. Translation: CAA34893.1.
PIRiS16603.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2AKJX-ray2.80A33-594[»]
ProteinModelPortaliP05314.
SMRiP05314. Positions 54-588.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

UniPathwayiUPA00653.
BRENDAi1.7.7.1. 5812.

Miscellaneous databases

EvolutionaryTraceiP05314.

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

  1. "Isolation of cDNA clones coding for spinach nitrite reductase: complete sequence and nitrate induction."
    Back E., Burkhart W., Moyer M., Privalle L., Rothstein S.
    Mol. Gen. Genet. 212:20-26(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], PARTIAL PROTEIN SEQUENCE.
  2. "Isolation of the spinach nitrite reductase gene promoter which confers nitrate inducibility on GUS gene expression in transgenic tobacco."
    Back E., Dunne W., Schneiderbauer A., de Framond A., Rastogi R., Rothstein S.J.
    Plant Mol. Biol. 17:9-18(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: cv. Dark green Bloomsdale.
    Tissue: Leaf.
  3. "Structure of spinach nitrite reductase: implications for multi-electron reactions by the iron-sulfur:siroheme cofactor."
    Swamy U., Wang M., Tripathy J.N., Kim S.K., Hirasawa M., Knaff D.B., Allen J.P.
    Biochemistry 44:16054-16063(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS), IRON-CLUSTER BINDING AT CYS-473; CYS-479; CYS-514 AND CYS-518, HEME BINDING AT CYS-518.

Entry informationi

Entry nameiNIR_SPIOL
AccessioniPrimary (citable) accession number: P05314
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1988
Last sequence update: November 1, 1988
Last modified: October 14, 2015
This is version 109 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

3D-structure, Direct protein sequencing

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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.