NIA_ULVPR
ID NIA_ULVPR Reviewed; 863 AA.
AC A0A286R227;
DT 17-JUN-2020, integrated into UniProtKB/Swiss-Prot.
DT 22-NOV-2017, sequence version 1.
DT 03-AUG-2022, entry version 22.
DE RecName: Full=Nitrate reductase [NADH] {ECO:0000305};
DE Short=NR {ECO:0000303|PubMed:28650572};
DE EC=1.7.1.1 {ECO:0000269|PubMed:29371148};
OS Ulva prolifera (Green seaweed) (Enteromorpha prolifera).
OC Eukaryota; Viridiplantae; Chlorophyta; Ulvophyceae; OUU clade; Ulvales;
OC Ulvaceae; Ulva.
OX NCBI_TaxID=3117;
RN [1] {ECO:0000312|EMBL:ASV49154.1}
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], AND INDUCTION.
RX PubMed=28650572; DOI=10.1111/jpy.12556;
RA Guo Y., Wang H.Z., Wu C.H., Fu H.H., Jiang P.;
RT "Cloning and characterization of nitrate reductase gene in Ulva prolifera
RT (Ulvophyceae, Chlorophyta).";
RL J. Phycol. 53:1035-1043(2017).
RN [2] {ECO:0007744|PDB:5YLY}
RP X-RAY CRYSTALLOGRAPHY (1.76 ANGSTROMS) OF 572-863 IN COMPLEX WITH FAD,
RP CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF
RP HIS-640; ARG-659; THR-662 AND CYS-835, AND 3D-STRUCTURE MODELING OF THE
RP FAD-BINDING DOMAIN IN COMPLEX WITH CYTOCHROME B5 FRAGMENT.
RX PubMed=29371148; DOI=10.1016/j.ijbiomac.2018.01.140;
RA You C., Liu C., Li Y., Jiang P., Ma Q.;
RT "Structural and enzymatic analysis of the cytochrome b5 reductase domain of
RT Ulva prolifera nitrate reductase.";
RL Int. J. Biol. Macromol. 111:1175-1182(2018).
CC -!- FUNCTION: Nitrate reductase is a key enzyme involved in the first step
CC of nitrate assimilation in plants, fungi and bacteria. {ECO:0000305}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + NAD(+) + nitrite = H(+) + NADH + nitrate;
CC Xref=Rhea:RHEA:17913, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16301, ChEBI:CHEBI:17632, ChEBI:CHEBI:57540,
CC ChEBI:CHEBI:57945; EC=1.7.1.1;
CC Evidence={ECO:0000269|PubMed:29371148};
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692;
CC Evidence={ECO:0000269|PubMed:29371148};
CC Note=Binds 1 FAD (per monomer/chain). {ECO:0000269|PubMed:29371148};
CC -!- COFACTOR:
CC Name=Mo-molybdopterin; Xref=ChEBI:CHEBI:71302;
CC Evidence={ECO:0000250|UniProtKB:P49050};
CC Note=Binds 1 Mo-molybdopterin (Mo-MPT) cofactor per subunit.
CC {ECO:0000250|UniProtKB:P49050};
CC -!- COFACTOR:
CC Name=heme; Xref=ChEBI:CHEBI:30413;
CC Evidence={ECO:0000305|PubMed:29371148};
CC Note=Binds 1 heme group. The heme group is called cytochrome b-557.
CC {ECO:0000305};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=13 uM for NADH in the ferricyanide reduction by the FAD-binding
CC domain (at ph 7.0 and 25 degrees Celsius)
CC {ECO:0000269|PubMed:29371148};
CC Vmax=9055 umol/min/mg enzyme in the ferricyanide reduction by the
CC FAD-binding domain (at ph 7.0 and 25 degrees Celsius)
CC {ECO:0000269|PubMed:29371148};
CC Note=kcat is 4900 sec(-1) for NADH in the ferricyanide reduction by
CC the FAD-binding domain (at ph 7.0 and 25 degrees Celsius).
CC {ECO:0000269|PubMed:29371148};
CC -!- SUBUNIT: Homodimer. {ECO:0000305}.
CC -!- INDUCTION: By nitrate. Repressed by ammonium, the repression is not
CC removed by the addition of extra nitrate. Urea weakens the effect of
CC nitrate, but does not repress expression itself, implying it possibly
CC reduces nitrate uptake rather than nitrate reduction. Up-regulated by
CC nitrite. {ECO:0000269|PubMed:28650572}.
CC -!- SIMILARITY: Belongs to the nitrate reductase family. {ECO:0000305}.
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DR EMBL; KY438973; ASV49153.1; -; Genomic_DNA.
DR EMBL; KY438974; ASV49154.1; -; mRNA.
DR PDB; 5YLY; X-ray; 1.76 A; A/B=572-863.
DR PDBsum; 5YLY; -.
DR AlphaFoldDB; A0A286R227; -.
DR SMR; A0A286R227; -.
DR GO; GO:0071949; F:FAD binding; IDA:UniProtKB.
DR GO; GO:0020037; F:heme binding; IEA:InterPro.
DR GO; GO:0030151; F:molybdenum ion binding; ISS:UniProtKB.
DR GO; GO:0043546; F:molybdopterin cofactor binding; ISS:UniProtKB.
DR GO; GO:0009703; F:nitrate reductase (NADH) activity; IEA:UniProtKB-EC.
DR GO; GO:0008940; F:nitrate reductase activity; IDA:UniProtKB.
DR GO; GO:0071250; P:cellular response to nitrite; IEP:UniProtKB.
DR GO; GO:0042128; P:nitrate assimilation; IEA:UniProtKB-KW.
DR GO; GO:0042126; P:nitrate metabolic process; IEP:UniProtKB.
DR Gene3D; 3.10.120.10; -; 1.
DR Gene3D; 3.40.50.80; -; 1.
DR Gene3D; 3.90.420.10; -; 1.
DR InterPro; IPR001834; CBR-like.
DR InterPro; IPR008333; Cbr1-like_FAD-bd_dom.
DR InterPro; IPR001199; Cyt_B5-like_heme/steroid-bd.
DR InterPro; IPR036400; Cyt_B5-like_heme/steroid_sf.
DR InterPro; IPR018506; Cyt_B5_heme-BS.
DR InterPro; IPR017927; FAD-bd_FR_type.
DR InterPro; IPR001709; Flavoprot_Pyr_Nucl_cyt_Rdtase.
DR InterPro; IPR039261; FNR_nucleotide-bd.
DR InterPro; IPR014756; Ig_E-set.
DR InterPro; IPR005066; MoCF_OxRdtse_dimer.
DR InterPro; IPR008335; Mopterin_OxRdtase_euk.
DR InterPro; IPR001433; OxRdtase_FAD/NAD-bd.
DR InterPro; IPR000572; OxRdtase_Mopterin-bd_dom.
DR InterPro; IPR036374; OxRdtase_Mopterin-bd_sf.
DR InterPro; IPR022407; OxRdtase_Mopterin_BS.
DR InterPro; IPR017938; Riboflavin_synthase-like_b-brl.
DR PANTHER; PTHR19370; PTHR19370; 1.
DR Pfam; PF00173; Cyt-b5; 1.
DR Pfam; PF00970; FAD_binding_6; 1.
DR Pfam; PF03404; Mo-co_dimer; 1.
DR Pfam; PF00175; NAD_binding_1; 1.
DR Pfam; PF00174; Oxidored_molyb; 1.
DR PRINTS; PR00363; CYTOCHROMEB5.
DR PRINTS; PR00407; EUMOPTERIN.
DR PRINTS; PR00371; FPNCR.
DR SMART; SM01117; Cyt-b5; 1.
DR SUPFAM; SSF52343; SSF52343; 1.
DR SUPFAM; SSF55856; SSF55856; 1.
DR SUPFAM; SSF56524; SSF56524; 1.
DR SUPFAM; SSF63380; SSF63380; 1.
DR SUPFAM; SSF81296; SSF81296; 1.
DR PROSITE; PS00191; CYTOCHROME_B5_1; 1.
DR PROSITE; PS50255; CYTOCHROME_B5_2; 1.
DR PROSITE; PS51384; FAD_FR; 1.
DR PROSITE; PS00559; MOLYBDOPTERIN_EUK; 1.
PE 1: Evidence at protein level;
KW 3D-structure; FAD; Flavoprotein; Heme; Iron; Metal-binding; Molybdenum;
KW Nitrate assimilation; Oxidoreductase.
FT CHAIN 1..863
FT /note="Nitrate reductase [NADH]"
FT /id="PRO_0000450331"
FT DOMAIN 484..559
FT /note="Cytochrome b5 heme-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00279"
FT DOMAIN 602..719
FT /note="FAD-binding FR-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00716"
FT BINDING 137
FT /ligand="Mo-molybdopterin"
FT /ligand_id="ChEBI:CHEBI:71302"
FT /ligand_part="Mo"
FT /ligand_part_id="ChEBI:CHEBI:28685"
FT /evidence="ECO:0000250|UniProtKB:P49050"
FT BINDING 519
FT /ligand="heme"
FT /ligand_id="ChEBI:CHEBI:30413"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00279"
FT BINDING 542
FT /ligand="heme"
FT /ligand_id="ChEBI:CHEBI:30413"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00279"
FT BINDING 659..662
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:29371148,
FT ECO:0007744|PDB:5YLY"
FT BINDING 676..680
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:29371148,
FT ECO:0007744|PDB:5YLY"
FT BINDING 688
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:29371148,
FT ECO:0007744|PDB:5YLY"
FT BINDING 693..695
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:29371148,
FT ECO:0007744|PDB:5YLY"
FT BINDING 746
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:29371148,
FT ECO:0007744|PDB:5YLY"
FT MUTAGEN 640
FT /note="H->A: Minimal effect in enzyme activity and a minor
FT change in affinity for NADH."
FT /evidence="ECO:0000269|PubMed:29371148"
FT MUTAGEN 659
FT /note="R->A: Loss of enzyme activity to 13% of that of the
FT wild-type and decreased affinity for NADH."
FT /evidence="ECO:0000269|PubMed:29371148"
FT MUTAGEN 662
FT /note="T->A: Loss of enzyme activity to 18% of that of the
FT wild-type and decreased affinity for NADH."
FT /evidence="ECO:0000269|PubMed:29371148"
FT MUTAGEN 835
FT /note="C->A: Loss of enzyme activity to 21% of that of the
FT wild-type, but increased affinity for NADH."
FT /evidence="ECO:0000269|PubMed:29371148"
FT STRAND 605..616
FT /evidence="ECO:0007829|PDB:5YLY"
FT STRAND 619..625
FT /evidence="ECO:0007829|PDB:5YLY"
FT STRAND 640..646
FT /evidence="ECO:0007829|PDB:5YLY"
FT STRAND 656..661
FT /evidence="ECO:0007829|PDB:5YLY"
FT STRAND 671..678
FT /evidence="ECO:0007829|PDB:5YLY"
FT STRAND 684..687
FT /evidence="ECO:0007829|PDB:5YLY"
FT HELIX 693..700
FT /evidence="ECO:0007829|PDB:5YLY"
FT STRAND 706..713
FT /evidence="ECO:0007829|PDB:5YLY"
FT STRAND 715..720
FT /evidence="ECO:0007829|PDB:5YLY"
FT STRAND 723..726
FT /evidence="ECO:0007829|PDB:5YLY"
FT STRAND 729..732
FT /evidence="ECO:0007829|PDB:5YLY"
FT STRAND 734..741
FT /evidence="ECO:0007829|PDB:5YLY"
FT HELIX 742..744
FT /evidence="ECO:0007829|PDB:5YLY"
FT HELIX 745..756
FT /evidence="ECO:0007829|PDB:5YLY"
FT STRAND 764..773
FT /evidence="ECO:0007829|PDB:5YLY"
FT HELIX 774..776
FT /evidence="ECO:0007829|PDB:5YLY"
FT HELIX 780..789
FT /evidence="ECO:0007829|PDB:5YLY"
FT TURN 791..793
FT /evidence="ECO:0007829|PDB:5YLY"
FT STRAND 794..802
FT /evidence="ECO:0007829|PDB:5YLY"
FT STRAND 809..813
FT /evidence="ECO:0007829|PDB:5YLY"
FT HELIX 816..822
FT /evidence="ECO:0007829|PDB:5YLY"
FT STRAND 830..836
FT /evidence="ECO:0007829|PDB:5YLY"
FT HELIX 838..843
FT /evidence="ECO:0007829|PDB:5YLY"
FT HELIX 846..851
FT /evidence="ECO:0007829|PDB:5YLY"
FT TURN 856..858
FT /evidence="ECO:0007829|PDB:5YLY"
FT STRAND 859..862
FT /evidence="ECO:0007829|PDB:5YLY"
SQ SEQUENCE 863 AA; 95563 MW; 644219E1578CDF84 CRC64;
MGVRHSASKD YIAGRPLVPG EAPLDKKNSN FSSWKPVTEI DDRDAKCADN WVPRHPDLIR
LTGKHPFNSE PPHADVMKEG WLTPVSMHFV RNHGAVPRLE WGSHRITITG LVERPMEITM
DDIAKLPAVT VPCLLTCCGN RRKEVNMVKN SQGFSWGPGA VSVNNWTGAR LSDVLKLVGV
KSQAQGAKYV HFCGPKGELP KGVDGSYGTA LTLGHALDPS MDVLIAYKQN GQFLHPDHGF
PCRMLIPGWI GGRSVKWLSH LHVSDKDSQN WYHFHDNKVL PPHVDAESAA KQGWWKDPSF
ILKELNINST ISSPGHDERI LMDQNRRYTM KGYAYSGGGR KIVRVEVSFN GGETWSHPAK
IIVTETPNQA GKHWTWVHWE LPVDTSQFFT ATEVVCRAWD ESQNTQPAVL TWTLLGQGNN
SMFRLRLHKE VDPQGRLCIR FQQPAPILPG PLGNVGWREQ EAGSAVPSAP AAVAAAAPGL
DSTKKYVTKA MLEQHVEEAS VWFAYKGKVY DGTKFLDDHP GGADSILMAG GEDATEDFDA
VHSDSAKKQL EQFYIAELAP EGVPVPANLL YGGVDAAVVV MPGTAAAPLP AIDVDAPFLN
PKKQKAAELK EKIKISHDVT LFRFGLEHDE QLLGLPTGKH MLIRKKVTNA EGDEEVVMRA
YTPTTANETR GHFDLVVKIY KANVHPKFPE GGKFSQILEA LEVGDTVEVK GPIGHFHYDR
PGHYKNHKLE SEVKRINMIA GGTGLTPMYQ VMKAILSNPS DLTEIRLLYA NQTEADILLR
PELEALAKSH PDRVKIHYTV DRPTPGWKYS SGFIDLDMCE RALFRYEPGT ISVLCGPPPM
LKFACHPNLE KMGFEKGVTS IEF
