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Riboflavin kinase (EC 2.7.1.26) (ATP:riboflavin 5'-phosphotransferase) (Flavokinase)

 RIFK_HUMAN              Reviewed;         155 AA.
Q969G6; Q5JSG9; Q9NUT7;
03-OCT-2003, integrated into UniProtKB/Swiss-Prot.
14-OCT-2008, sequence version 2.
12-AUG-2020, entry version 169.
RecName: Full=Riboflavin kinase;
EC=2.7.1.26;
AltName: Full=ATP:riboflavin 5'-phosphotransferase;
AltName: Full=Flavokinase;
Name=RFK;
Homo sapiens (Human).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
Homo.
NCBI_TaxID=9606;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
TISSUE=Placenta;
PubMed=14702039; DOI=10.1038/ng1285;
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H.,
Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M.,
Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K.,
Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T.,
Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M.,
Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S.,
Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H.,
Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K.,
Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N.,
Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y.,
Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K.,
Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T.,
Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T.,
Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y.,
Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H.,
Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y.,
Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H.,
Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O.,
Isogai T., Sugano S.;
"Complete sequencing and characterization of 21,243 full-length human
cDNAs.";
Nat. Genet. 36:40-45(2004).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
PubMed=15164053; DOI=10.1038/nature02465;
Humphray S.J., Oliver K., Hunt A.R., Plumb R.W., Loveland J.E., Howe K.L.,
Andrews T.D., Searle S., Hunt S.E., Scott C.E., Jones M.C., Ainscough R.,
Almeida J.P., Ambrose K.D., Ashwell R.I.S., Babbage A.K., Babbage S.,
Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K.,
Beasley H., Beasley O., Bird C.P., Bray-Allen S., Brown A.J., Brown J.Y.,
Burford D., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C.,
Chen Y., Clarke G., Clark S.Y., Clee C.M., Clegg S., Collier R.E.,
Corby N., Crosier M., Cummings A.T., Davies J., Dhami P., Dunn M.,
Dutta I., Dyer L.W., Earthrowl M.E., Faulkner L., Fleming C.J.,
Frankish A., Frankland J.A., French L., Fricker D.G., Garner P.,
Garnett J., Ghori J., Gilbert J.G.R., Glison C., Grafham D.V., Gribble S.,
Griffiths C., Griffiths-Jones S., Grocock R., Guy J., Hall R.E.,
Hammond S., Harley J.L., Harrison E.S.I., Hart E.A., Heath P.D.,
Henderson C.D., Hopkins B.L., Howard P.J., Howden P.J., Huckle E.,
Johnson C., Johnson D., Joy A.A., Kay M., Keenan S., Kershaw J.K.,
Kimberley A.M., King A., Knights A., Laird G.K., Langford C., Lawlor S.,
Leongamornlert D.A., Leversha M., Lloyd C., Lloyd D.M., Lovell J.,
Martin S., Mashreghi-Mohammadi M., Matthews L., McLaren S., McLay K.E.,
McMurray A., Milne S., Nickerson T., Nisbett J., Nordsiek G., Pearce A.V.,
Peck A.I., Porter K.M., Pandian R., Pelan S., Phillimore B., Povey S.,
Ramsey Y., Rand V., Scharfe M., Sehra H.K., Shownkeen R., Sims S.K.,
Skuce C.D., Smith M., Steward C.A., Swarbreck D., Sycamore N., Tester J.,
Thorpe A., Tracey A., Tromans A., Thomas D.W., Wall M., Wallis J.M.,
West A.P., Whitehead S.L., Willey D.L., Williams S.A., Wilming L.,
Wray P.W., Young L., Ashurst J.L., Coulson A., Blocker H., Durbin R.M.,
Sulston J.E., Hubbard T., Jackson M.J., Bentley D.R., Beck S., Rogers J.,
Dunham I.;
"DNA sequence and analysis of human chromosome 9.";
Nature 429:369-374(2004).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
TISSUE=Urinary bladder;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA project:
the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[4]
FUNCTION, INTERACTION WITH CYBA; TNFRSF1A AND TRADD, AND MUTAGENESIS OF
GLU-79.
PubMed=19641494; DOI=10.1038/nature08206;
Yazdanpanah B., Wiegmann K., Tchikov V., Krut O., Pongratz C., Schramm M.,
Kleinridders A., Wunderlich T., Kashkar H., Utermoehlen O., Bruening J.C.,
Schuetze S., Kroenke M.;
"Riboflavin kinase couples TNF receptor 1 to NADPH oxidase.";
Nature 460:1159-1163(2009).
[5]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=21269460; DOI=10.1186/1752-0509-5-17;
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T.,
Bennett K.L., Superti-Furga G., Colinge J.;
"Initial characterization of the human central proteome.";
BMC Syst. Biol. 5:17-17(2011).
[6]
X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 2-148 IN COMPLEX WITH MG-ADP AND
RIBOFLAVIN NUCLEOTIDE.
PubMed=12623014; DOI=10.1016/s0969-2126(03)00024-8;
Karthikeyan S., Zhou Q., Mseeh F., Grishin N.V., Osterman A.L., Zhang H.;
"Crystal structure of human riboflavin kinase reveals a beta barrel fold
and a novel active site arch.";
Structure 11:265-273(2003).
-!- FUNCTION: Catalyzes the phosphorylation of riboflavin (vitamin B2) to
form flavin-mononucleotide (FMN), hence rate-limiting enzyme in the
synthesis of FAD. Essential for TNF-induced reactive oxygen species
(ROS) production. Through its interaction with both TNFRSF1A and CYBA,
physically and functionally couples TNFRSF1A to NADPH oxidase. TNF-
activation of RFK may enhance the incorporation of FAD in NADPH
oxidase, a critical step for the assembly and activation of NADPH
oxidase. {ECO:0000269|PubMed:19641494}.
-!- CATALYTIC ACTIVITY:
Reaction=ATP + riboflavin = ADP + FMN + H(+); Xref=Rhea:RHEA:14357,
ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:57986,
ChEBI:CHEBI:58210, ChEBI:CHEBI:456216; EC=2.7.1.26;
-!- COFACTOR:
Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Note=Zinc or magnesium.;
-!- PATHWAY: Cofactor biosynthesis; FMN biosynthesis; FMN from riboflavin
(ATP route): step 1/1.
-!- SUBUNIT: Monomer. Directly interacts with TNFRSF1A death domain.
TNFRSF1A-binding may be supported by TRADD. In the absence of TNFRSF1A,
interacts with TRADD. Independently of TNFRSF1A, interacts with the
NADPH oxidase subunit CYBA. {ECO:0000269|PubMed:12623014,
ECO:0000269|PubMed:19641494}.
-!- INTERACTION:
Q969G6; P19438: TNFRSF1A; NbExp=4; IntAct=EBI-716872, EBI-299451;
Q969G6; P19438-1: TNFRSF1A; NbExp=2; IntAct=EBI-716872, EBI-15795644;
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
-!- TISSUE SPECIFICITY: Detected in brain, placenta and urinary bladder.
-!- SEQUENCE CAUTION:
Sequence=AAH07069.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
Sequence=BAA92033.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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EMBL; AK002011; BAA92033.1; ALT_INIT; mRNA.
EMBL; AL391868; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; BC007069; AAH07069.1; ALT_INIT; mRNA.
CCDS; CCDS35044.2; -.
RefSeq; NP_060809.3; NM_018339.5.
PDB; 1NB0; X-ray; 1.70 A; A=2-148.
PDB; 1NB9; X-ray; 1.70 A; A=2-148.
PDB; 1P4M; X-ray; 1.80 A; A=2-148.
PDB; 1Q9S; X-ray; 2.42 A; A=1-148.
PDBsum; 1NB0; -.
PDBsum; 1NB9; -.
PDBsum; 1P4M; -.
PDBsum; 1Q9S; -.
SMR; Q969G6; -.
BioGRID; 120594; 11.
DIP; DIP-60454N; -.
IntAct; Q969G6; 5.
STRING; 9606.ENSP00000365926; -.
DrugBank; DB03247; Flavin mononucleotide.
DrugBank; DB00140; Riboflavin.
DrugCentral; Q969G6; -.
iPTMnet; Q969G6; -.
PhosphoSitePlus; Q969G6; -.
BioMuta; RFK; -.
DMDM; 209572667; -.
EPD; Q969G6; -.
jPOST; Q969G6; -.
MassIVE; Q969G6; -.
MaxQB; Q969G6; -.
PaxDb; Q969G6; -.
PeptideAtlas; Q969G6; -.
PRIDE; Q969G6; -.
ProteomicsDB; 75757; -.
Antibodypedia; 27259; 147 antibodies.
DNASU; 55312; -.
Ensembl; ENST00000376736; ENSP00000365926; ENSG00000135002.
GeneID; 55312; -.
KEGG; hsa:55312; -.
UCSC; uc004akd.3; human.
CTD; 55312; -.
DisGeNET; 55312; -.
EuPathDB; HostDB:ENSG00000135002.11; -.
GeneCards; RFK; -.
HGNC; HGNC:30324; RFK.
HPA; ENSG00000135002; Low tissue specificity.
MIM; 613010; gene.
neXtProt; NX_Q969G6; -.
OpenTargets; ENSG00000135002; -.
PharmGKB; PA134916697; -.
eggNOG; KOG3110; Eukaryota.
GeneTree; ENSGT00390000015537; -.
HOGENOM; CLU_048437_3_3_1; -.
InParanoid; Q969G6; -.
KO; K00861; -.
OMA; EDIRVDC; -.
OrthoDB; 1534271at2759; -.
PhylomeDB; Q969G6; -.
TreeFam; TF313786; -.
BioCyc; MetaCyc:HS05938-MONOMER; -.
BRENDA; 2.7.1.26; 2681.
PathwayCommons; Q969G6; -.
Reactome; R-HSA-196843; Vitamin B2 (riboflavin) metabolism.
UniPathway; UPA00276; UER00406.
BioGRID-ORCS; 55312; 234 hits in 851 CRISPR screens.
ChiTaRS; RFK; human.
EvolutionaryTrace; Q969G6; -.
GenomeRNAi; 55312; -.
Pharos; Q969G6; Tbio.
PRO; PR:Q969G6; -.
Proteomes; UP000005640; Chromosome 9.
RNAct; Q969G6; protein.
Bgee; ENSG00000135002; Expressed in colonic mucosa and 254 other tissues.
ExpressionAtlas; Q969G6; baseline and differential.
Genevisible; Q969G6; HS.
GO; GO:0005737; C:cytoplasm; NAS:UniProtKB.
GO; GO:0005829; C:cytosol; TAS:Reactome.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0008531; F:riboflavin kinase activity; IBA:GO_Central.
GO; GO:0006915; P:apoptotic process; IMP:MGI.
GO; GO:0009398; P:FMN biosynthetic process; IBA:GO_Central.
GO; GO:0033864; P:positive regulation of NAD(P)H oxidase activity; IMP:MGI.
GO; GO:0072593; P:reactive oxygen species metabolic process; IEA:Ensembl.
GO; GO:0009231; P:riboflavin biosynthetic process; NAS:UniProtKB.
GO; GO:0006771; P:riboflavin metabolic process; IBA:GO_Central.
Gene3D; 2.40.30.30; -; 1.
InterPro; IPR023468; Riboflavin_kinase.
InterPro; IPR015865; Riboflavin_kinase_bac/euk.
InterPro; IPR023465; Riboflavin_kinase_dom_sf.
PANTHER; PTHR22749; PTHR22749; 1.
Pfam; PF01687; Flavokinase; 1.
SMART; SM00904; Flavokinase; 1.
SUPFAM; SSF82114; SSF82114; 1.
1: Evidence at protein level;
3D-structure; ATP-binding; Cytoplasm; Flavoprotein; FMN; Kinase; Magnesium;
Metal-binding; Nucleotide-binding; Reference proteome; Transferase; Zinc.
CHAIN 1..155
/note="Riboflavin kinase"
/id="PRO_0000194148"
ACT_SITE 79
/note="Nucleophile"
/evidence="ECO:0000250"
METAL 27
/note="Magnesium"
BINDING 15
/note="ATP; via amide nitrogen"
BINDING 21
/note="ATP; via amide nitrogen"
BINDING 27
/note="ATP; via amide nitrogen"
BINDING 29
/note="ATP"
BINDING 82
/note="ATP; via amide nitrogen and carbonyl oxygen"
BINDING 84
/note="ATP; via carbonyl oxygen"
BINDING 91
/note="ATP"
BINDING 104
/note="FMN"
BINDING 107
/note="FMN; via amide nitrogen and carbonyl oxygen"
BINDING 109
/note="FMN; via amide nitrogen"
MUTAGEN 79
/note="E->Q: Loss of kinase activity. No effect on
TNFRSF1A- and CYBA-binding."
/evidence="ECO:0000269|PubMed:19641494"
CONFLICT 96
/note="N -> S (in Ref. 1; BAA92033)"
/evidence="ECO:0000305"
STRAND 5..11
/evidence="ECO:0000244|PDB:1NB0"
STRAND 16..18
/evidence="ECO:0000244|PDB:1NB0"
HELIX 20..23
/evidence="ECO:0000244|PDB:1NB0"
HELIX 32..36
/evidence="ECO:0000244|PDB:1NB0"
STRAND 44..53
/evidence="ECO:0000244|PDB:1NB0"
STRAND 59..67
/evidence="ECO:0000244|PDB:1NB0"
STRAND 69..74
/evidence="ECO:0000244|PDB:1NB0"
STRAND 76..84
/evidence="ECO:0000244|PDB:1NB0"
STRAND 93..104
/evidence="ECO:0000244|PDB:1NB0"
HELIX 112..129
/evidence="ECO:0000244|PDB:1NB0"
HELIX 133..136
/evidence="ECO:0000244|PDB:1NB0"
HELIX 137..140
/evidence="ECO:0000244|PDB:1NB0"
HELIX 142..146
/evidence="ECO:0000244|PDB:1NB0"
SEQUENCE 155 AA; 17623 MW; 3E038E487E164EBA CRC64;
MRHLPYFCRG QVVRGFGRGS KQLGIPTANF PEQVVDNLPA DISTGIYYGW ASVGSGDVHK
MVVSIGWNPY YKNTKKSMET HIMHTFKEDF YGEILNVAIV GYLRPEKNFD SLESLISAIQ
GDIEEAKKRL ELPEHLKIKE DNFFQVSKSK IMNGH


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