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Protein

Solute carrier family 52, riboflavin transporter, member 3

Gene

SLC52A3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Transporter for riboflavin, which must be obtained as a nutrient via intestinal absorption. Riboflavin transport is Na+-independent at low pH but significantly reduced by Na+ depletion under neutral pH conditions. Activity is strongly inhibited by riboflavin analogs, such as lumiflavin, flavin mononucleotide (FMN), flavin adenine dinucleotide (FAD), by methylene blue, and to a lesser extent by amiloride.2 Publications

Kineticsi

  1. KM=0.98 µM for riboflavin1 Publication

    GO - Molecular functioni

    • riboflavin transporter activity Source: UniProtKB

    GO - Biological processi

    • cellular response to heat Source: Ensembl
    • riboflavin metabolic process Source: Reactome
    • riboflavin transport Source: UniProtKB
    • sensory perception of sound Source: UniProtKB
    Complete GO annotation...

    Keywords - Biological processi

    Transport

    Enzyme and pathway databases

    BioCyciZFISH:ENSG00000101276-MONOMER.
    ReactomeiR-HSA-196843. Vitamin B2 (riboflavin) metabolism.

    Protein family/group databases

    TCDBi2.A.125.1.2. the eukaryotic riboflavin transporter (e-rft) family.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Solute carrier family 52, riboflavin transporter, member 3
    Alternative name(s):
    Riboflavin transporter 2
    Short name:
    hRFT2
    Gene namesi
    Name:SLC52A3
    Synonyms:C20orf54, RFT2, RFVT3
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    Proteomesi
    • UP000005640 Componenti: Chromosome 20

    Organism-specific databases

    HGNCiHGNC:16187. SLC52A3.

    Subcellular locationi

    Topology

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Topological domaini1 – 2CytoplasmicSequence analysis2
    Transmembranei3 – 23HelicalSequence analysisAdd BLAST21
    Topological domaini24 – 43ExtracellularSequence analysisAdd BLAST20
    Transmembranei44 – 64HelicalSequence analysisAdd BLAST21
    Topological domaini65 – 71CytoplasmicSequence analysis7
    Transmembranei72 – 92HelicalSequence analysisAdd BLAST21
    Topological domaini93 – 97ExtracellularSequence analysis5
    Transmembranei98 – 118HelicalSequence analysisAdd BLAST21
    Topological domaini119 – 137CytoplasmicSequence analysisAdd BLAST19
    Transmembranei138 – 158HelicalSequence analysisAdd BLAST21
    Topological domaini159 – 220ExtracellularSequence analysisAdd BLAST62
    Transmembranei221 – 241HelicalSequence analysisAdd BLAST21
    Topological domaini242 – 292CytoplasmicSequence analysisAdd BLAST51
    Transmembranei293 – 313HelicalSequence analysisAdd BLAST21
    Topological domaini314 – 335ExtracellularSequence analysisAdd BLAST22
    Transmembranei336 – 356HelicalSequence analysisAdd BLAST21
    Topological domaini357 – 359CytoplasmicSequence analysis3
    Transmembranei360 – 380HelicalSequence analysisAdd BLAST21
    Topological domaini381 – 396ExtracellularSequence analysisAdd BLAST16
    Transmembranei397 – 417HelicalSequence analysisAdd BLAST21
    Topological domaini418 – 427CytoplasmicSequence analysis10
    Transmembranei428 – 448HelicalSequence analysisAdd BLAST21
    Topological domaini449 – 469ExtracellularSequence analysisAdd BLAST21

    GO - Cellular componenti

    • apical plasma membrane Source: UniProtKB-SubCell
    • integral component of plasma membrane Source: UniProtKB
    • plasma membrane Source: Reactome
    Complete GO annotation...

    Keywords - Cellular componenti

    Cell membrane, Membrane

    Pathology & Biotechi

    Involvement in diseasei

    Brown-Vialetto-Van Laere syndrome 1 (BVVLS1)1 Publication
    The disease is caused by mutations affecting the gene represented in this entry.
    Disease descriptionA rare neurologic disorder characterized by sensorineural hearing loss and a variety of cranial nerve palsies, which develop over a relatively short period of time in a previously healthy individual. Sensorineural hearing loss may precede the neurological signs. The course is invariably progressive, but the rate of decline is variable within and between families. With disease evolution, long tract signs, lower motor neuron signs, cerebellar ataxia and lower cranial nerve (III-VI) palsies develop, giving rise to a complex picture resembling amyotrophic lateral sclerosis. Diaphragmatic weakness and respiratory compromise are some of the most distressing features, leading to recurrent chest infections and respiratory failure, which are often the cause of patients' demise.
    See also OMIM:211530
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Natural variantiVAR_06369436E → K in BVVLS1. 1 PublicationCorresponds to variant rs267606686dbSNPEnsembl.1
    Natural variantiVAR_063695132R → W in BVVLS1. 1 PublicationCorresponds to variant rs267606684dbSNPEnsembl.1
    Natural variantiVAR_063696224F → L in BVVLS1. 1 PublicationCorresponds to variant rs267606685dbSNPEnsembl.1
    Natural variantiVAR_063700413V → A in BVVLS1; may cause a mild form of the disease. 1 PublicationCorresponds to variant rs267606687dbSNPEnsembl.1
    Natural variantiVAR_063701457F → L in BVVLS1. 1 PublicationCorresponds to variant rs779750163dbSNPEnsembl.1
    Fazio-Londe disease (FALOND)1 Publication
    The disease is caused by mutations affecting the gene represented in this entry.
    Disease descriptionA rare neurological disease characterized by progressive weakness of the muscles innervated by cranial nerves of the lower brain stem. It may present in childhood with severe neurological deterioration with hypotonia, respiratory insufficiency leading to premature death, or later in life with bulbar weakness which progresses to involve motor neurons throughout the neuroaxis. Clinical manifestations include dysarthria, dysphagia, facial weakness, tongue weakness, and fasciculations of the tongue and facial muscles.
    See also OMIM:211500

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi326C → A: No effect on cell surface localization. 1 Publication1
    Mutagenesisi386C → A: Abolishes cell surface localization. 1 Publication1
    Mutagenesisi455R → A: No effect on cell surface localization. 1 Publication1
    Mutagenesisi463C → A: Abolishes cell surface localization. 1 Publication1
    Mutagenesisi467C → A: Abolishes cell surface localization. 1 Publication1

    Keywords - Diseasei

    Deafness, Disease mutation

    Organism-specific databases

    DisGeNETi113278.
    MalaCardsiSLC52A3.
    MIMi211500. phenotype.
    211530. phenotype.
    OpenTargetsiENSG00000101276.
    Orphaneti97229. Riboflavin transporter deficiency.
    PharmGKBiPA25764.

    Polymorphism and mutation databases

    BioMutaiSLC52A3.
    DMDMi82654931.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000426361 – 469Solute carrier family 52, riboflavin transporter, member 3Add BLAST469

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Glycosylationi94N-linked (GlcNAc...)Sequence analysis1
    Glycosylationi168N-linked (GlcNAc...)Sequence analysis1
    Modified residuei251PhosphoserineBy similarity1
    Disulfide bondi386 ↔ 4631 Publication

    Keywords - PTMi

    Disulfide bond, Glycoprotein, Phosphoprotein

    Proteomic databases

    PaxDbiQ9NQ40.
    PeptideAtlasiQ9NQ40.
    PRIDEiQ9NQ40.

    PTM databases

    PhosphoSitePlusiQ9NQ40.

    Expressioni

    Tissue specificityi

    Predominantly expressed in testis. Highly expressed in small intestine and prostate.1 Publication

    Gene expression databases

    BgeeiENSG00000101276.
    CleanExiHS_C20orf54.
    ExpressionAtlasiQ9NQ40. baseline and differential.
    GenevisibleiQ9NQ40. HS.

    Organism-specific databases

    HPAiHPA049391.

    Interactioni

    Protein-protein interaction databases

    STRINGi9606.ENSP00000217254.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9NQ40.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the riboflavin transporter family.Curated

    Keywords - Domaini

    Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiKOG4255. Eukaryota.
    ENOG410YE1U. LUCA.
    GeneTreeiENSGT00390000003774.
    HOGENOMiHOG000247012.
    HOVERGENiHBG051170.
    InParanoidiQ9NQ40.
    KOiK14620.
    OMAiAMFLHFT.
    OrthoDBiEOG091G0BZA.
    PhylomeDBiQ9NQ40.
    TreeFamiTF314820.

    Family and domain databases

    InterProiIPR009357. Riboflavin_transptr.
    [Graphical view]
    PANTHERiPTHR12929. PTHR12929. 2 hits.
    PfamiPF06237. DUF1011. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

    Isoform 1 (identifier: Q9NQ40-1) [UniParc]FASTAAdd to basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

            10         20         30         40         50
    MAFLMHLLVC VFGMGSWVTI NGLWVELPLL VMELPEGWYL PSYLTVVIQL
    60 70 80 90 100
    ANIGPLLVTL LHHFRPSCLS EVPIIFTLLG VGTVTCIIFA FLWNMTSWVL
    110 120 130 140 150
    DGHHSIAFLV LTFFLALVDC TSSVTFLPFM SRLPTYYLTT FFVGEGLSGL
    160 170 180 190 200
    LPALVALAQG SGLTTCVNVT EISDSVPSPV PTRETDIAQG VPRALVSALP
    210 220 230 240 250
    GMEAPLSHLE SRYLPAHFSP LVFFLLLSIM MACCLVAFFV LQRQPRCWEA
    260 270 280 290 300
    SVEDLLNDQV TLHSIRPREE NDLGPAGTVD SSQGQGYLEE KAAPCCPAHL
    310 320 330 340 350
    AFIYTLVAFV NALTNGMLPS VQTYSCLSYG PVAYHLAATL SIVANPLASL
    360 370 380 390 400
    VSMFLPNRSL LFLGVLSVLG TCFGGYNMAM AVMSPCPLLQ GHWGGEVLIV
    410 420 430 440 450
    ASWVLFSGCL SYVKVMLGVV LRDLSRSALL WCGAAVQLGS LLGALLMFPL
    460
    VNVLRLFSSA DFCNLHCPA
    Length:469
    Mass (Da):50,805
    Last modified:November 22, 2005 - v4
    Checksum:i239ED67348C93739
    GO
    Isoform 2 (identifier: Q9NQ40-2) [UniParc]FASTAAdd to basket

    The sequence of this isoform differs from the canonical sequence as follows:
         401-415: ASWVLFSGCLSYVKV → SIRPVGLLPLRTPHP
         416-469: Missing.

    Note: No experimental confirmation available.
    Show »
    Length:415
    Mass (Da):45,043
    Checksum:i8E072208A8998A56
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti11V → D in BAF84395 (PubMed:14702039).Curated1
    Sequence conflicti199L → P in BAC11113 (PubMed:14702039).Curated1

    Natural variant

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Natural variantiVAR_06369436E → K in BVVLS1. 1 PublicationCorresponds to variant rs267606686dbSNPEnsembl.1
    Natural variantiVAR_05356574I → M.Corresponds to variant rs35655964dbSNPEnsembl.1
    Natural variantiVAR_063695132R → W in BVVLS1. 1 PublicationCorresponds to variant rs267606684dbSNPEnsembl.1
    Natural variantiVAR_053566174D → G.Corresponds to variant rs6054614dbSNPEnsembl.1
    Natural variantiVAR_063696224F → L in BVVLS1. 1 PublicationCorresponds to variant rs267606685dbSNPEnsembl.1
    Natural variantiVAR_053567267P → L.1 PublicationCorresponds to variant rs3746804dbSNPEnsembl.1
    Natural variantiVAR_053568278T → M.1 PublicationCorresponds to variant rs3746803dbSNPEnsembl.1
    Natural variantiVAR_053569303I → V.1 PublicationCorresponds to variant rs3746802dbSNPEnsembl.1
    Natural variantiVAR_063698350L → M May be a common polymorphism. 1 PublicationCorresponds to variant rs76947760dbSNPEnsembl.1
    Natural variantiVAR_063699411S → R.Corresponds to variant rs910857dbSNPEnsembl.1
    Natural variantiVAR_063700413V → A in BVVLS1; may cause a mild form of the disease. 1 PublicationCorresponds to variant rs267606687dbSNPEnsembl.1
    Natural variantiVAR_063701457F → L in BVVLS1. 1 PublicationCorresponds to variant rs779750163dbSNPEnsembl.1

    Alternative sequence

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Alternative sequenceiVSP_003814401 – 415ASWVL…SYVKV → SIRPVGLLPLRTPHP in isoform 2. 1 PublicationAdd BLAST15
    Alternative sequenceiVSP_003815416 – 469Missing in isoform 2. 1 PublicationAdd BLAST54

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AK074650 mRNA. Translation: BAC11113.1.
    AK291706 mRNA. Translation: BAF84395.1.
    AL118502 Genomic DNA. Translation: CAH73077.2.
    AL118502 Genomic DNA. Translation: CAH73078.2.
    BC009750 mRNA. Translation: AAH09750.2.
    CCDSiCCDS13007.1. [Q9NQ40-1]
    RefSeqiNP_212134.3. NM_033409.3. [Q9NQ40-1]
    XP_005260712.1. XM_005260655.3. [Q9NQ40-1]
    XP_011527450.1. XM_011529148.1. [Q9NQ40-1]
    UniGeneiHs.283865.

    Genome annotation databases

    EnsembliENST00000217254; ENSP00000217254; ENSG00000101276. [Q9NQ40-1]
    ENST00000381944; ENSP00000371370; ENSG00000101276. [Q9NQ40-2]
    ENST00000632431; ENSP00000488723; ENSG00000101276. [Q9NQ40-1]
    GeneIDi113278.
    KEGGihsa:113278.
    UCSCiuc002wed.5. human. [Q9NQ40-1]

    Keywords - Coding sequence diversityi

    Alternative splicing, Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AK074650 mRNA. Translation: BAC11113.1.
    AK291706 mRNA. Translation: BAF84395.1.
    AL118502 Genomic DNA. Translation: CAH73077.2.
    AL118502 Genomic DNA. Translation: CAH73078.2.
    BC009750 mRNA. Translation: AAH09750.2.
    CCDSiCCDS13007.1. [Q9NQ40-1]
    RefSeqiNP_212134.3. NM_033409.3. [Q9NQ40-1]
    XP_005260712.1. XM_005260655.3. [Q9NQ40-1]
    XP_011527450.1. XM_011529148.1. [Q9NQ40-1]
    UniGeneiHs.283865.

    3D structure databases

    ProteinModelPortaliQ9NQ40.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi9606.ENSP00000217254.

    Protein family/group databases

    TCDBi2.A.125.1.2. the eukaryotic riboflavin transporter (e-rft) family.

    PTM databases

    PhosphoSitePlusiQ9NQ40.

    Polymorphism and mutation databases

    BioMutaiSLC52A3.
    DMDMi82654931.

    Proteomic databases

    PaxDbiQ9NQ40.
    PeptideAtlasiQ9NQ40.
    PRIDEiQ9NQ40.

    Protocols and materials databases

    DNASUi113278.
    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsembliENST00000217254; ENSP00000217254; ENSG00000101276. [Q9NQ40-1]
    ENST00000381944; ENSP00000371370; ENSG00000101276. [Q9NQ40-2]
    ENST00000632431; ENSP00000488723; ENSG00000101276. [Q9NQ40-1]
    GeneIDi113278.
    KEGGihsa:113278.
    UCSCiuc002wed.5. human. [Q9NQ40-1]

    Organism-specific databases

    CTDi113278.
    DisGeNETi113278.
    GeneCardsiSLC52A3.
    H-InvDBHIX0015557.
    HGNCiHGNC:16187. SLC52A3.
    HPAiHPA049391.
    MalaCardsiSLC52A3.
    MIMi211500. phenotype.
    211530. phenotype.
    613350. gene.
    neXtProtiNX_Q9NQ40.
    OpenTargetsiENSG00000101276.
    Orphaneti97229. Riboflavin transporter deficiency.
    PharmGKBiPA25764.
    GenAtlasiSearch...

    Phylogenomic databases

    eggNOGiKOG4255. Eukaryota.
    ENOG410YE1U. LUCA.
    GeneTreeiENSGT00390000003774.
    HOGENOMiHOG000247012.
    HOVERGENiHBG051170.
    InParanoidiQ9NQ40.
    KOiK14620.
    OMAiAMFLHFT.
    OrthoDBiEOG091G0BZA.
    PhylomeDBiQ9NQ40.
    TreeFamiTF314820.

    Enzyme and pathway databases

    BioCyciZFISH:ENSG00000101276-MONOMER.
    ReactomeiR-HSA-196843. Vitamin B2 (riboflavin) metabolism.

    Miscellaneous databases

    GeneWikiiC20orf54.
    GenomeRNAii113278.
    PROiQ9NQ40.
    SOURCEiSearch...

    Gene expression databases

    BgeeiENSG00000101276.
    CleanExiHS_C20orf54.
    ExpressionAtlasiQ9NQ40. baseline and differential.
    GenevisibleiQ9NQ40. HS.

    Family and domain databases

    InterProiIPR009357. Riboflavin_transptr.
    [Graphical view]
    PANTHERiPTHR12929. PTHR12929. 2 hits.
    PfamiPF06237. DUF1011. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiS52A3_HUMAN
    AccessioniPrimary (citable) accession number: Q9NQ40
    Secondary accession number(s): A8K6P1
    , Q5W1A0, Q5W1A1, Q8NCL7, Q96GD5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 10, 2003
    Last sequence update: November 22, 2005
    Last modified: November 2, 2016
    This is version 129 of the entry and version 4 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program
    DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

    Miscellaneousi

    Caution

    It is uncertain whether Met-1 or Met-5 is the initiator.Curated

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Human chromosome 20
      Human chromosome 20: entries, gene names and cross-references to MIM
    2. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    3. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    4. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    5. 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.