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NADH-cytochrome b5 reductase 3 (B5R) (Cytochrome b5 reductase) (EC 1.6.2.2) (Diaphorase-1) (Fragment)

 NB5R3_PIG               Reviewed;         272 AA.
P83686;
15-DEC-2003, integrated into UniProtKB/Swiss-Prot.
15-DEC-2003, sequence version 1.
22-NOV-2017, entry version 101.
RecName: Full=NADH-cytochrome b5 reductase 3;
Short=B5R;
Short=Cytochrome b5 reductase;
EC=1.6.2.2;
AltName: Full=Diaphorase-1;
Flags: Fragment;
Name=CYB5R3; Synonyms=DIA1;
Sus scrofa (Pig).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Laurasiatheria; Cetartiodactyla; Suina; Suidae;
Sus.
NCBI_TaxID=9823 {ECO:0000312|PDB:1NDH};
[1] {ECO:0000305}
NUCLEOTIDE SEQUENCE, PROTEIN SEQUENCE OF 1-5, MUTAGENESIS OF HIS-49
AND PHE-272, AND CIRCULAR DICHROISM ANALYSIS.
TISSUE=Liver {ECO:0000269|PubMed:10082957};
PubMed=10082957; DOI=10.1016/S0167-4838(99)00008-4;
Kimura S., Emi Y., Ikushiro S., Iyanagi T.;
"Systematic mutations of highly conserved His49 and carboxyl-terminal
of recombinant porcine liver NADH-cytochrome b5 reductase solubilized
domain.";
Biochim. Biophys. Acta 1430:290-301(1999).
[2] {ECO:0000305}
PROTEIN SEQUENCE OF 1-20.
TISSUE=Liver {ECO:0000269|PubMed:7417338};
PubMed=7417338; DOI=10.1016/S0006-291X(80)80088-X;
Crabb J.W., Tarr G.E., Yasunobu K.T., Iyanagi T., Coon M.J.;
"Terminal sequences of lysosome solubilized pig liver cytochrome b5
reductase.";
Biochem. Biophys. Res. Commun. 95:1650-1655(1980).
[3] {ECO:0000305}
CHARACTERIZATION.
PubMed=3967486;
Ghesquier D., Robert J.C., Soumarmon A., Abastado M., Grelac F.,
Lewin M.J.M.;
"Gastric microsomal NADH-cytochrome b5 reductase: characterization and
solubilization.";
Comp. Biochem. Physiol. 80B:165-169(1985).
[4] {ECO:0000305}
FAD-BINDING.
PubMed=7890048; DOI=10.1016/0014-5793(95)00161-2;
Nishida H., Inaka K., Miki K.;
"Specific arrangement of three amino acid residues for flavin-binding
barrel structures in NADH-cytochrome b5 reductase and the other
flavin-dependent reductases.";
FEBS Lett. 361:97-100(1995).
[5] {ECO:0000305}
POTENTIOMETRIC TITRATION, AND EPR SPECTROSCOPY.
PubMed=19038; DOI=10.1021/bi00631a021;
Iyanagi T.;
"Redox properties of microsomal reduced nicotinamide adenine
dinucleotide-cytochrome b5 reductase and cytochrome b5.";
Biochemistry 16:2725-2730(1977).
[6] {ECO:0000305}
ENZYME KINETICS.
PubMed=3372498;
Kobayashi K., Iyanagi T., Ohara H., Hayashi K.;
"One-electron reduction of hepatic NADH-cytochrome b5 reductase as
studied by pulse radiolysis.";
J. Biol. Chem. 263:7493-7499(1988).
[7] {ECO:0000305}
MUTAGENESIS OF ARG-63; TYR-65; LYS-97 AND SER-99, AND CIRCULAR
DICHROISM ANALYSIS.
PubMed=11574067; DOI=10.1093/oxfordjournals.jbchem.a003010;
Kimura S., Nishida H., Iyanagi T.;
"Effects of flavin-binding motif amino acid mutations in the NADH-
cytochrome b5 reductase catalytic domain on protein stability and
catalysis.";
J. Biochem. 130:481-490(2001).
[8] {ECO:0000305}
MUTAGENESIS OF THR-66, ENZYME KINETICS, AND CIRCULAR DICHROISM
ANALYSIS.
PubMed=12459552; DOI=10.1074/jbc.M209838200;
Kimura S., Kawamura M., Iyanagi T.;
"Role of Thr(66) in porcine NADH-cytochrome b5 reductase in catalysis
and control of the rate-limiting step in electron transfer.";
J. Biol. Chem. 278:3580-3589(2003).
[9]
IDENTIFICATION IN A COMPLEX WITH CYTOCHROME B5 AND MOSC2.
PubMed=16973608; DOI=10.1074/jbc.M607697200;
Havemeyer A., Bittner F., Wollers S., Mendel R., Kunze T., Clement B.;
"Identification of the missing component in the mitochondrial
benzamidoxime prodrug converting system as a novel molybdenum
enzyme.";
J. Biol. Chem. 281:34796-34802(2006).
[10] {ECO:0000312|PDB:1NDH}
X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 2-273.
PubMed=7893687; DOI=10.1021/bi00009a004;
Nishida H., Inaka K., Yamanaka M., Kaida S., Kobayashi K., Miki K.;
"Crystal structure of NADH-cytochrome b5 reductase from pig liver at
2.4 A resolution.";
Biochemistry 34:2763-2767(1995).
[11] {ECO:0000305}
X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS), AND 3D-STRUCTURE MODELING OF
COMPLEX WITH CYTOCHROME B5.
PubMed=8880927;
DOI=10.1002/(SICI)1097-0134(199609)26:1<32::AID-PROT3>3.0.CO;2-I;
Nishida H., Miki K.;
"Electrostatic properties deduced from refined structures of NADH-
cytochrome b5 reductase and the other flavin-dependent reductases:
pyridine nucleotide-binding and interaction with an electron-transfer
partner.";
Proteins 26:32-41(1996).
-!- FUNCTION: Desaturation and elongation of fatty acids, cholesterol
biosynthesis, drug metabolism, and, in erythrocyte, methemoglobin
reduction. {ECO:0000305}.
-!- CATALYTIC ACTIVITY: NADH + 2 ferricytochrome b5 = NAD(+) + H(+) +
2 ferrocytochrome b5.
-!- COFACTOR:
Name=FAD; Xref=ChEBI:CHEBI:57692;
Evidence={ECO:0000269|PubMed:7890048};
-!- SUBUNIT: Component of a complex composed of cytochrome b5, NADH-
cytochrome b5 reductase (CYB5R3) and MOSC2.
{ECO:0000269|PubMed:16973608}.
-!- SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
{ECO:0000250|UniProtKB:P00387}; Lipid-anchor
{ECO:0000250|UniProtKB:P00387}; Cytoplasmic side
{ECO:0000250|UniProtKB:P00387}. Mitochondrion outer membrane
{ECO:0000250|UniProtKB:P00387}; Lipid-anchor
{ECO:0000250|UniProtKB:P00387}; Cytoplasmic side
{ECO:0000250|UniProtKB:P00387}. Cytoplasm
{ECO:0000250|UniProtKB:P00387}. Note=The enzyme exists in two
forms, a membrane-bound form on the cytoplasmic side of the
endoplasmic reticulum and also on the mitochondrial outer membrane
and in soluble form in erythrocytes. NADH-cytochrome b5 reductase
3 membrane-bound form: Endoplasmic reticulum membrane; Lipid-
anchor; Cytoplasmic side. Mitochondrion outer membrane; Lipid-
anchor; Cytoplasmic side. NADH-cytochrome b5 reductase 3 soluble
form: Cytoplasm. {ECO:0000250|UniProtKB:P00387}.
-!- SIMILARITY: Belongs to the flavoprotein pyridine nucleotide
cytochrome reductase family. {ECO:0000305}.
-----------------------------------------------------------------------
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PDB; 1NDH; X-ray; 2.10 A; A=1-272.
PDB; 3W2E; X-ray; 2.10 A; A=2-272.
PDB; 3W2F; X-ray; 1.76 A; A=2-272.
PDB; 3W2G; X-ray; 1.68 A; A=2-272.
PDB; 3W2H; X-ray; 1.75 A; A=2-272.
PDB; 3W2I; X-ray; 1.81 A; A=2-272.
PDB; 3W5H; X-ray; 0.78 A; A=1-272.
PDB; 5GV7; X-ray; 0.80 A; A=1-272.
PDB; 5GV8; X-ray; 0.78 A; A=1-272.
PDBsum; 1NDH; -.
PDBsum; 3W2E; -.
PDBsum; 3W2F; -.
PDBsum; 3W2G; -.
PDBsum; 3W2H; -.
PDBsum; 3W2I; -.
PDBsum; 3W5H; -.
PDBsum; 5GV7; -.
PDBsum; 5GV8; -.
ProteinModelPortal; P83686; -.
SMR; P83686; -.
STRING; 9823.ENSSSCP00000000040; -.
PaxDb; P83686; -.
PeptideAtlas; P83686; -.
PRIDE; P83686; -.
eggNOG; KOG0534; Eukaryota.
eggNOG; COG0543; LUCA.
HOGENOM; HOG000175005; -.
HOVERGEN; HBG052580; -.
InParanoid; P83686; -.
BRENDA; 1.6.2.2; 6170.
SABIO-RK; P83686; -.
EvolutionaryTrace; P83686; -.
Proteomes; UP000008227; Unplaced.
GO; GO:0005789; C:endoplasmic reticulum membrane; IEA:UniProtKB-SubCell.
GO; GO:0005741; C:mitochondrial outer membrane; IEA:UniProtKB-SubCell.
GO; GO:0004128; F:cytochrome-b5 reductase activity, acting on NAD(P)H; IDA:UniProtKB.
GO; GO:0050660; F:flavin adenine dinucleotide binding; IDA:UniProtKB.
GO; GO:0006695; P:cholesterol biosynthetic process; IEA:UniProtKB-KW.
InterPro; IPR017927; Fd_Rdtase_FAD-bd.
InterPro; IPR001709; Flavoprot_Pyr_Nucl_cyt_Rdtase.
InterPro; IPR001834; NADH-Cyt_B5_reductase.
InterPro; IPR008333; OxRdtase_FAD-bd_dom.
InterPro; IPR001433; OxRdtase_FAD/NAD-bd.
InterPro; IPR017938; Riboflavin_synthase-like_b-brl.
Pfam; PF00970; FAD_binding_6; 1.
Pfam; PF00175; NAD_binding_1; 1.
PRINTS; PR00406; CYTB5RDTASE.
PRINTS; PR00371; FPNCR.
SUPFAM; SSF63380; SSF63380; 1.
PROSITE; PS51384; FAD_FR; 1.
1: Evidence at protein level;
3D-structure; Acetylation; Cholesterol biosynthesis;
Cholesterol metabolism; Complete proteome; Cytoplasm;
Direct protein sequencing; Endoplasmic reticulum; FAD; Flavoprotein;
Lipid biosynthesis; Lipid metabolism; Lipoprotein; Membrane;
Mitochondrion; Mitochondrion outer membrane; NAD; Oxidoreductase;
Phosphoprotein; Reference proteome; Steroid biosynthesis;
Steroid metabolism; Sterol biosynthesis; Sterol metabolism.
CHAIN <1 272 NADH-cytochrome b5 reductase 3.
/FTId=PRO_0000167625.
DOMAIN 11 123 FAD-binding FR-type.
{ECO:0000255|PROSITE-ProRule:PRU00716}.
NP_BIND 103 118 FAD. {ECO:0000250}.
NP_BIND 142 177 FAD. {ECO:0000250}.
MOD_RES 13 13 N6-acetyllysine.
{ECO:0000250|UniProtKB:P00387}.
MOD_RES 14 14 Phosphotyrosine.
{ECO:0000250|UniProtKB:P00387}.
MOD_RES 21 21 N6-acetyllysine.
{ECO:0000250|UniProtKB:Q9DCN2}.
MOD_RES 91 91 N6-acetyllysine.
{ECO:0000250|UniProtKB:Q9DCN2}.
MUTAGEN 49 49 H->A: Similar properties to wild-type.
{ECO:0000269|PubMed:10082957}.
MUTAGEN 49 49 H->E: Decreased Kcat values for PB5,
ferricyanide and NADH. Increased Km
values for all three substrates.
{ECO:0000269|PubMed:10082957}.
MUTAGEN 49 49 H->K: Decreased Kcat and Km values for
PB5 and ferricyanide. Increased values
for NADH. {ECO:0000269|PubMed:10082957}.
MUTAGEN 49 49 H->Y: Similar properties to wild-type.
{ECO:0000269|PubMed:10082957}.
MUTAGEN 63 63 R->A,Q: Increased Km values for NADH and
increased dissociation constant for
NAD(+). {ECO:0000269|PubMed:11574067}.
MUTAGEN 63 63 R->K: Little effect on Km and KD values.
{ECO:0000269|PubMed:11574067}.
MUTAGEN 65 65 Y->A,F: Protein destabilized, release of
FAD accelerated, and Kcat values
decreased. {ECO:0000269|PubMed:11574067}.
MUTAGEN 66 66 T->A: Similar properties to wild-type.
{ECO:0000269|PubMed:12459552}.
MUTAGEN 66 66 T->S: Similar properties to wild-type.
{ECO:0000269|PubMed:12459552}.
MUTAGEN 66 66 T->V: 10% of wild-type Kcat values.
{ECO:0000269|PubMed:12459552}.
MUTAGEN 97 97 K->A: Little effect on absorption or CD
spectra. {ECO:0000269|PubMed:11574067}.
MUTAGEN 97 97 K->R: Little effect on absorption or CD
spectra. {ECO:0000269|PubMed:11574067}.
MUTAGEN 99 99 S->A,V: Increased Km values for NADH and
increased dissociation constant for
NAD(+). {ECO:0000269|PubMed:11574067}.
MUTAGEN 99 99 S->T: Little effect on Km and KD values.
{ECO:0000269|PubMed:11574067}.
MUTAGEN 272 272 F->FG: 10% of wild-type Kcat values.
{ECO:0000269|PubMed:10082957}.
MUTAGEN 272 272 Missing: 54% of wild-type Kcat values.
{ECO:0000269|PubMed:10082957}.
CONFLICT 39 39 E -> Q (in Ref. 1). {ECO:0000305}.
NON_TER 1 1
STRAND 14 25 {ECO:0000244|PDB:3W5H}.
STRAND 28 34 {ECO:0000244|PDB:3W5H}.
STRAND 49 56 {ECO:0000244|PDB:3W5H}.
STRAND 59 65 {ECO:0000244|PDB:3W5H}.
STRAND 67 69 {ECO:0000244|PDB:3W2E}.
STRAND 75 82 {ECO:0000244|PDB:3W5H}.
TURN 86 88 {ECO:0000244|PDB:3W2G}.
STRAND 89 91 {ECO:0000244|PDB:1NDH}.
HELIX 97 104 {ECO:0000244|PDB:3W5H}.
STRAND 110 117 {ECO:0000244|PDB:3W5H}.
STRAND 119 124 {ECO:0000244|PDB:3W5H}.
STRAND 127 130 {ECO:0000244|PDB:3W5H}.
STRAND 132 135 {ECO:0000244|PDB:1NDH}.
STRAND 139 142 {ECO:0000244|PDB:3W5H}.
STRAND 144 151 {ECO:0000244|PDB:3W5H}.
HELIX 152 154 {ECO:0000244|PDB:3W5H}.
HELIX 155 166 {ECO:0000244|PDB:3W5H}.
STRAND 174 183 {ECO:0000244|PDB:3W5H}.
HELIX 184 186 {ECO:0000244|PDB:3W5H}.
HELIX 190 200 {ECO:0000244|PDB:3W5H}.
TURN 201 203 {ECO:0000244|PDB:3W5H}.
STRAND 204 212 {ECO:0000244|PDB:3W5H}.
STRAND 218 223 {ECO:0000244|PDB:3W5H}.
HELIX 226 232 {ECO:0000244|PDB:3W5H}.
HELIX 236 238 {ECO:0000244|PDB:3W5H}.
STRAND 241 246 {ECO:0000244|PDB:3W5H}.
HELIX 248 253 {ECO:0000244|PDB:3W5H}.
HELIX 256 262 {ECO:0000244|PDB:3W5H}.
HELIX 266 268 {ECO:0000244|PDB:3W5H}.
STRAND 269 271 {ECO:0000244|PDB:5GV7}.
SEQUENCE 272 AA; 30831 MW; 16B08682FC365090 CRC64;
STPAITLENP DIKYPLRLID KEVVNHDTRR FRFALPSPEH ILGLPVGQHI YLSARIDGNL
VIRPYTPVSS DDDKGFVDLV IKVYFKDTHP KFPAGGKMSQ YLESMKIGDT IEFRGPNGLL
VYQGKGKFAI RPDKKSSPVI KTVKSVGMIA GGTGITPMLQ VIRAIMKDPD DHTVCHLLFA
NQTEKDILLR PELEELRNEH SARFKLWYTV DRAPEAWDYS QGFVNEEMIR DHLPPPEEEP
LVLMCGPPPM IQYACLPNLE RVGHPKERCF AF


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