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Assimilatory ferredoxin-dependent nitrite reductase (NiR) (EC 1.7.7.1) (Ferredoxin:nitrite reductase)

 NASD_HALMT              Reviewed;         586 AA.
I3R637; Q703N2;
14-MAY-2014, integrated into UniProtKB/Swiss-Prot.
05-SEP-2012, sequence version 1.
05-DEC-2018, entry version 39.
RecName: Full=Assimilatory ferredoxin-dependent nitrite reductase {ECO:0000303|PubMed:16182473};
Short=NiR {ECO:0000303|PubMed:16182473};
EC=1.7.7.1 {ECO:0000269|PubMed:11267765};
AltName: Full=Ferredoxin:nitrite reductase {ECO:0000305};
Name=nasD {ECO:0000303|PubMed:16182473};
Synonyms=fdx-niR {ECO:0000312|EMBL:CAF19045.1};
OrderedLocusNames=HFX_2005; ORFNames=C439_11803;
Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM 8866 / NBRC
14739 / NCIMB 2177 / R-4) (Halobacterium mediterranei).
Archaea; Euryarchaeota; Stenosarchaea group; Halobacteria;
Haloferacales; Haloferacaceae; Haloferax.
NCBI_TaxID=523841;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, INDUCTION, AND PATHWAY.
STRAIN=ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 /
R-4;
PubMed=16182473; DOI=10.1016/j.gene.2005.07.011;
Lledo B., Marhuenda-Egea F.C., Martinez-Espinosa R.M., Bonete M.J.;
"Identification and transcriptional analysis of nitrate assimilation
genes in the halophilic archaeon Haloferax mediterranei.";
Gene 361:80-88(2005).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 /
R-4;
PubMed=22843593; DOI=10.1128/JB.00880-12;
Han J., Zhang F., Hou J., Liu X., Li M., Liu H., Cai L., Zhang B.,
Chen Y., Zhou J., Hu S., Xiang H.;
"Complete genome sequence of the metabolically versatile halophilic
archaeon Haloferax mediterranei, a poly(3-hydroxybutyrate-co-3-
hydroxyvalerate) producer.";
J. Bacteriol. 194:4463-4464(2012).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 /
R-4;
Becker E.A., Seitzer P., Tritt A., Larsen D., Yao A., Wu D.,
Darling A., Eisen J.A., Facciotti M.T.;
Submitted (NOV-2012) to the EMBL/GenBank/DDBJ databases.
[4]
FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, COFACTOR,
SUBUNIT, ACTIVITY REGULATION, AND BIOPHYSICOCHEMICAL PROPERTIES.
PubMed=11267765; DOI=10.1111/j.1574-6968.2001.tb10550.x;
Martinez-Espinosa R.M., Marhuenda-Egea F.C., Bonete M.J.;
"Purification and characterisation of a possible assimilatory nitrite
reductase from the halophile archaeon Haloferax mediterranei.";
FEMS Microbiol. Lett. 196:113-118(2001).
-!- FUNCTION: Catalyzes the reduction of nitrite to ammonium in the
nitrate assimilation pathway, using ferredoxin as the electron
donor. Can use reduced methyl viologen but neither NADPH nor NADH
as electron donors. {ECO:0000269|PubMed:11267765}.
-!- CATALYTIC ACTIVITY:
Reaction=2 H2O + NH4(+) + 6 oxidized [2Fe-2S]-[ferredoxin] = 8
H(+) + nitrite + 6 reduced [2Fe-2S]-[ferredoxin];
Xref=Rhea:RHEA:18041, Rhea:RHEA-COMP:10000, Rhea:RHEA-
COMP:10001, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
ChEBI:CHEBI:16301, ChEBI:CHEBI:28938, ChEBI:CHEBI:33737,
ChEBI:CHEBI:33738; EC=1.7.7.1;
Evidence={ECO:0000269|PubMed:11267765};
-!- COFACTOR:
Name=siroheme; Xref=ChEBI:CHEBI:60052;
Evidence={ECO:0000269|PubMed:11267765};
Note=Binds 1 siroheme per subunit. {ECO:0000250|UniProtKB:P9WJ03};
-!- COFACTOR:
Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
Evidence={ECO:0000305|PubMed:11267765};
Note=Binds 1 [4Fe-4S] cluster per subunit.;
-!- ACTIVITY REGULATION: Inhibited by cyanide and azide.
{ECO:0000269|PubMed:11267765}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=8.6 mM for nitrite {ECO:0000269|PubMed:11267765};
KM=1.9 mM for methyl viologen {ECO:0000269|PubMed:11267765};
Vmax=4.1 umol/min/mg enzyme with nitrite as substrate
{ECO:0000269|PubMed:11267765};
Vmax=1.7 umol/min/mg enzyme with methyl viologen as substrate
{ECO:0000269|PubMed:11267765};
Note=In the presence of 3.2 M NaCl.;
pH dependence:
Optimum pH is 7.5 at 60 degrees Celsius. At 40 degrees Celsius
(temperature of the natural environment for H.mediterranei) the
optimum pH is 6.5. {ECO:0000269|PubMed:11267765};
Temperature dependence:
Optimum temperature is 60 degrees Celsius.
{ECO:0000269|PubMed:11267765};
-!- PATHWAY: Nitrogen metabolism; nitrate reduction (assimilation).
{ECO:0000305|PubMed:16182473}.
-!- SUBUNIT: Monomer. {ECO:0000269|PubMed:11267765}.
-!- INDUCTION: Repressed by the presence of ammonium as nitrogen
source. {ECO:0000269|PubMed:16182473}.
-!- MISCELLANEOUS: Enzyme stability and activity depend upon the salt
concentration. {ECO:0000269|PubMed:11267765}.
-!- SIMILARITY: Belongs to the nitrite and sulfite reductase 4Fe-4S
domain family. {ECO:0000305}.
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EMBL; AJ621501; CAF19045.1; -; Genomic_DNA.
EMBL; CP001868; AFK19697.1; -; Genomic_DNA.
EMBL; AOLO01000009; EMA00019.1; -; Genomic_DNA.
RefSeq; WP_004059343.1; NZ_CP007551.1.
SMR; I3R637; -.
EnsemblBacteria; AFK19697; AFK19697; HFX_2005.
EnsemblBacteria; EMA00019; EMA00019; C439_11803.
GeneID; 13028165; -.
KEGG; hme:HFX_2005; -.
KO; K00366; -.
OMA; CNFALIE; -.
OrthoDB; POG093Z01X5; -.
BioCyc; HMED523841:G1HBL-2725-MONOMER; -.
UniPathway; UPA00653; -.
Proteomes; UP000006469; Chromosome.
Proteomes; UP000011603; Unassembled WGS sequence.
GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
GO; GO:0048307; F:ferredoxin-nitrite reductase activity; IEA:UniProtKB-EC.
GO; GO:0020037; F:heme binding; IEA:InterPro.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0016491; F:oxidoreductase activity; IDA:CACAO.
GO; GO:0042128; P:nitrate assimilation; IEA:UniProtKB-UniPathway.
InterPro; IPR005117; NiRdtase/SiRdtase_haem-b_fer.
InterPro; IPR036136; Nit/Sulf_reduc_fer_like_dom_sf.
InterPro; IPR006067; NO2/SO3_Rdtase_4Fe4S_dom.
InterPro; IPR006066; NO2/SO3_Rdtase_FeS/sirohaem_BS.
Pfam; PF01077; NIR_SIR; 2.
Pfam; PF03460; NIR_SIR_ferr; 2.
PRINTS; PR00397; SIROHAEM.
SUPFAM; SSF55124; SSF55124; 2.
PROSITE; PS00365; NIR_SIR; 2.
1: Evidence at protein level;
4Fe-4S; Complete proteome; Electron transport; Heme; Iron;
Iron-sulfur; Metal-binding; Nitrate assimilation; Oxidoreductase;
Reference proteome; Transport.
CHAIN 1 586 Assimilatory ferredoxin-dependent nitrite
reductase.
/FTId=PRO_0000428891.
METAL 411 411 Iron-sulfur (4Fe-4S).
{ECO:0000250|UniProtKB:P9WJ03}.
METAL 417 417 Iron-sulfur (4Fe-4S).
{ECO:0000250|UniProtKB:P9WJ03}.
METAL 455 455 Iron-sulfur (4Fe-4S).
{ECO:0000250|UniProtKB:P9WJ03}.
METAL 459 459 Iron (siroheme axial ligand).
{ECO:0000250|UniProtKB:P9WJ03}.
METAL 459 459 Iron-sulfur (4Fe-4S).
{ECO:0000250|UniProtKB:P9WJ03}.
CONFLICT 175 175 D -> N (in Ref. 1; CAF19045).
{ECO:0000305}.
CONFLICT 205 217 LEPARKEVDGEVI -> WNPPGKRSTERLF (in Ref.
1; CAF19045). {ECO:0000305}.
CONFLICT 366 366 K -> Q (in Ref. 1; CAF19045).
{ECO:0000305}.
SEQUENCE 586 AA; 65438 MW; DCA1E981EE4B5210 CRC64;
MASKKEQWKS DLYGDAVRDE LEAFAEEGFE SIPEDERDKW FTRFKFWGVF QQRTGQESYF
MMRLTNANGV LEPGQLRTIA EVARDYATGP VDNPEFGNGW VDLTTRQSIQ LHWLELEDIP
EIWEQLESVG VTSRSAGGDT MRNITGCPVA GKDTHELVES KPLLDRFQSE LREDDALSNM
PRKFNISVTG CREGCAQDSI NDIGLEPARK EVDGEVITGF NVRVGGGLGS RKPRVARSLD
VFVADEERAY EVVRGFVELY HDHGNRDVRA RARSRFFVDD WGTEKIRDRL ESEYLDFELQ
SAGEDIRDEY TYNAGRPQSA GKSDHVGVHE QSDGRYYVGL SVAVGRLTAA DALELADLAD
KYGSGKIRLT RRQNPIVMDV PAGALDDLLA EPLLSKHTPE PNPFQRGTVA CTGTEFCSLA
LTETKARTAR MLRWLRDNVE VPDDVHQLKI HYSGCTADCG QANTADIGLF GMRAQKDGEM
VEAMDIGVGG GIGDEPSFVE WIHQRVPADE VPGAIASLVE AFAAHRTAGQ TFRQWVEAEG
PDAVAEYCEP IETDFEAPYM HDAKQSWYPF ADEDEPPKTE QPMTSD


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