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Protein

Ribokinase

Gene

RBKS

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

Functioni

Catalyzes the phosphorylation of ribose at O-5 in a reaction requiring ATP and magnesium. The resulting D-ribose-5-phosphate can then be used either for sythesis of nucleotides, histidine, and tryptophan, or as a component of the pentose phosphate pathway.UniRule annotation1 Publication

Catalytic activityi

ATP + D-ribose = ADP + D-ribose 5-phosphate.UniRule annotation1 Publication

Cofactori

Mg2+UniRule annotationNote: Requires a divalent cation, most likely magnesium in vivo, as an electrophilic catalyst to aid phosphoryl group transfer. It is the chelate of the metal and the nucleotide that is the actual substrate.UniRule annotation

Enzyme regulationi

Activated by a monovalent cation that binds near, but not in, the active site. The most likely occupant of the site in vivo is potassium. Ion binding induces a conformational change that may alter substrate affinity (By similarity). Competitively inhibited by phosphonoacetic acid, etidronate, 2-carboxethylphosphonic acid, N-(phosphonomethyl)glycine, N-(phosphonomethyl)iminodiacetic acid and clodronate (PubMed:17585908).UniRule annotation1 Publication

Kineticsi

  1. KM=2.17 mM for ribose (in the presence of 10 mM inorganic phosphate)1 Publication
  2. KM=3.39 mM for ribose (in the presence of 5 mM inorganic phosphate)1 Publication
  3. KM=6.62 mM for ribose (in the presence of 2 mM inorganic phosphate)1 Publication
  4. KM=30.43 mM for ribose (in the presence of 1 mM inorganic phosphate)1 Publication
  5. KM=0.07 mM for ATP (in the presence of 5 mM inorganic phosphate)1 Publication
  6. KM=0.08 mM for ATP (in the presence of 2 mM inorganic phosphate)1 Publication
  7. KM=0.10 mM for ATP (in the presence of 1 mM inorganic phosphate)1 Publication

    Pathwayi: D-ribose degradation

    This protein is involved in step 2 of the subpathway that synthesizes D-ribose 5-phosphate from beta-D-ribopyranose.UniRule annotation
    Proteins known to be involved in the 2 steps of the subpathway in this organism are:
    1. no protein annotated in this organism
    2. Ribokinase (RBKS)
    This subpathway is part of the pathway D-ribose degradation, which is itself part of Carbohydrate metabolism.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes D-ribose 5-phosphate from beta-D-ribopyranose, the pathway D-ribose degradation and in Carbohydrate metabolism.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei154SubstrateUniRule annotationBy similarity1
    Binding sitei199ATPUniRule annotation1 Publication1
    Binding sitei256ATPUniRule annotation1 Publication1
    Metal bindingi263PotassiumUniRule annotation1 Publication1
    Metal bindingi265Potassium; via carbonyl oxygenUniRule annotationBy similarity1
    Active sitei269Proton acceptorUniRule annotationBy similarity1
    Binding sitei269SubstrateUniRule annotationBy similarity1
    Binding sitei295ATPUniRule annotation1 Publication1
    Metal bindingi301Potassium; via carbonyl oxygenUniRule annotation1 Publication1
    Metal bindingi304Potassium; via carbonyl oxygenUniRule annotation1 Publication1
    Metal bindingi306Potassium; via carbonyl oxygenUniRule annotationBy similarity1
    Metal bindingi310PotassiumUniRule annotation1 Publication1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi235 – 240ATPUniRule annotation1 Publication6
    Nucleotide bindingi268 – 269ATPUniRule annotation1 Publication2

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Kinase, Transferase

    Keywords - Biological processi

    Carbohydrate metabolism

    Keywords - Ligandi

    ATP-binding, Magnesium, Metal-binding, Nucleotide-binding, Potassium

    Enzyme and pathway databases

    BioCyciZFISH:HS10260-MONOMER.
    UniPathwayiUPA00916; UER00889.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ribokinase1 PublicationUniRule annotation (EC:2.7.1.15UniRule annotation1 Publication)
    Short name:
    RK1 PublicationUniRule annotation
    Gene namesi
    Name:RBKSUniRule annotation
    Synonyms:RBSK
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    Proteomesi
    • UP000005640 Componenti: Chromosome 2

    Organism-specific databases

    HGNCiHGNC:30325. RBKS.

    Subcellular locationi

    • Cytoplasm UniRule annotationBy similarity
    • Nucleus UniRule annotationBy similarity

    GO - Cellular componenti

    • cytoplasm Source: UniProtKB-SubCell
    • extracellular exosome Source: UniProtKB
    • nucleus Source: UniProtKB-SubCell
    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    Pathology & Biotechi

    Organism-specific databases

    DisGeNETi64080.
    OpenTargetsiENSG00000171174.
    PharmGKBiPA134951602.

    Polymorphism and mutation databases

    DMDMi20139730.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000800921 – 322RibokinaseAdd BLAST322

    Proteomic databases

    EPDiQ9H477.
    MaxQBiQ9H477.
    PaxDbiQ9H477.
    PeptideAtlasiQ9H477.
    PRIDEiQ9H477.

    PTM databases

    iPTMnetiQ9H477.
    PhosphoSitePlusiQ9H477.

    Expressioni

    Gene expression databases

    BgeeiENSG00000171174.
    ExpressionAtlasiQ9H477. baseline and differential.
    GenevisibleiQ9H477. HS.

    Organism-specific databases

    HPAiHPA019725.
    HPA028285.

    Interactioni

    Subunit structurei

    Homodimer.UniRule annotationBy similarity

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    ACDQ96AP02EBI-10982959,EBI-717666

    Protein-protein interaction databases

    BioGridi122046. 10 interactors.
    IntActiQ9H477. 6 interactors.
    STRINGi9606.ENSP00000306817.

    Structurei

    Secondary structure

    1322
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi17 – 21Combined sources5
    Beta strandi25 – 31Combined sources7
    Beta strandi41 – 43Combined sources3
    Beta strandi45 – 52Combined sources8
    Helixi54 – 64Combined sources11
    Beta strandi69 – 78Combined sources10
    Helixi79 – 90Combined sources12
    Beta strandi98 – 101Combined sources4
    Beta strandi108 – 113Combined sources6
    Beta strandi119 – 124Combined sources6
    Helixi126 – 130Combined sources5
    Helixi133 – 138Combined sources6
    Helixi140 – 145Combined sources6
    Beta strandi147 – 151Combined sources5
    Beta strandi153 – 155Combined sources3
    Helixi157 – 169Combined sources13
    Beta strandi173 – 176Combined sources4
    Helixi188 – 191Combined sources4
    Beta strandi194 – 199Combined sources6
    Helixi200 – 207Combined sources8
    Helixi214 – 225Combined sources12
    Turni226 – 228Combined sources3
    Beta strandi230 – 235Combined sources6
    Helixi237 – 239Combined sources3
    Beta strandi241 – 247Combined sources7
    Beta strandi252 – 254Combined sources3
    Helixi267 – 281Combined sources15
    Helixi287 – 301Combined sources15
    Beta strandi304 – 306Combined sources3
    Helixi307 – 310Combined sources4
    Helixi314 – 316Combined sources3
    Helixi319 – 322Combined sources4

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2FV7X-ray2.10A/B11-322[»]
    5BYCX-ray1.95A/B1-322[»]
    5BYDX-ray2.10A/B1-322[»]
    5BYEX-ray1.75A/B1-322[»]
    5BYFX-ray2.00A/B1-322[»]
    5C3YX-ray2.60A/B/C/D/E/F/G/H/I/J/K/L1-322[»]
    5C3ZX-ray1.90A/B1-322[»]
    5C40X-ray1.50A/B1-322[»]
    5C41X-ray1.95A/B/C/D1-322[»]
    ProteinModelPortaliQ9H477.
    SMRiQ9H477.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9H477.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni25 – 27Substrate bindingUniRule annotationBy similarity3
    Regioni53 – 57Substrate bindingUniRule annotationBy similarity5

    Sequence similaritiesi

    Belongs to the carbohydrate kinase PfkB family. Ribokinase subfamily.UniRule annotation

    Phylogenomic databases

    eggNOGiKOG2855. Eukaryota.
    COG0524. LUCA.
    GeneTreeiENSGT00390000005743.
    HOGENOMiHOG000235950.
    HOVERGENiHBG018350.
    InParanoidiQ9H477.
    KOiK00852.
    OMAiNDSPFVA.
    OrthoDBiEOG091G08OZ.
    PhylomeDBiQ9H477.
    TreeFamiTF105770.

    Family and domain databases

    CDDicd01174. ribokinase. 1 hit.
    Gene3Di3.40.1190.20. 1 hit.
    HAMAPiMF_01987. Ribokinase. 1 hit.
    InterProiIPR002173. Carboh/pur_kinase_PfkB_CS.
    IPR011877. D_ribokin.
    IPR011611. PfkB_dom.
    IPR002139. Ribo/fructo_kinase.
    IPR029056. Ribokinase-like.
    [Graphical view]
    PfamiPF00294. PfkB. 1 hit.
    [Graphical view]
    PRINTSiPR00990. RIBOKINASE.
    SUPFAMiSSF53613. SSF53613. 1 hit.
    TIGRFAMsiTIGR02152. D_ribokin_bact. 1 hit.
    PROSITEiPS00584. PFKB_KINASES_2. 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: Q9H477-1) [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
    MAASGEPQRQ WQEEVAAVVV VGSCMTDLVS LTSRLPKTGE TIHGHKFFIG
    60 70 80 90 100
    FGGKGANQCV QAARLGAMTS MVCKVGKDSF GNDYIENLKQ NDISTEFTYQ
    110 120 130 140 150
    TKDAATGTAS IIVNNEGQNI IVIVAGANLL LNTEDLRAAA NVISRAKVMV
    160 170 180 190 200
    CQLEITPATS LEALTMARRS GVKTLFNPAP AIADLDPQFY TLSDVFCCNE
    210 220 230 240 250
    SEAEILTGLT VGSAADAGEA ALVLLKRGCQ VVIITLGAEG CVVLSQTEPE
    260 270 280 290 300
    PKHIPTEKVK AVDTTGAGDS FVGALAFYLA YYPNLSLEDM LNRSNFIAAV
    310 320
    SVQAAGTQSS YPYKKDLPLT LF
    Length:322
    Mass (Da):34,143
    Last modified:March 1, 2001 - v1
    Checksum:i50D0E7161F33E94B
    GO
    Isoform 2 (identifier: Q9H477-2) [UniParc]FASTAAdd to basket

    The sequence of this isoform differs from the canonical sequence as follows:
         266-322: GAGDSFVGAL...YKKDLPLTLF → CRPGSRPKSEAASVKKQKHYK

    Note: No experimental confirmation available.
    Show »
    Length:286
    Mass (Da):30,361
    Checksum:i020866FD563F058F
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti101T → A in AAT64917 (Ref. 2) Curated1

    Alternative sequence

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Alternative sequenceiVSP_054380266 – 322GAGDS…PLTLF → CRPGSRPKSEAASVKKQKHY K in isoform 2. 1 PublicationAdd BLAST57

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AJ404857 mRNA. Translation: CAC12877.1.
    AY643715 mRNA. Translation: AAT64917.1.
    AK300989 mRNA. Translation: BAG62608.1.
    AC021171 Genomic DNA. No translation available.
    AC110084 Genomic DNA. No translation available.
    BC017425 mRNA. Translation: AAH17425.1.
    CCDSiCCDS1762.1. [Q9H477-1]
    RefSeqiNP_001274509.1. NM_001287580.1.
    NP_071411.1. NM_022128.2. [Q9H477-1]
    UniGeneiHs.11916.

    Genome annotation databases

    EnsembliENST00000302188; ENSP00000306817; ENSG00000171174. [Q9H477-1]
    GeneIDi64080.
    KEGGihsa:64080.
    UCSCiuc002rlo.3. human. [Q9H477-1]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AJ404857 mRNA. Translation: CAC12877.1.
    AY643715 mRNA. Translation: AAT64917.1.
    AK300989 mRNA. Translation: BAG62608.1.
    AC021171 Genomic DNA. No translation available.
    AC110084 Genomic DNA. No translation available.
    BC017425 mRNA. Translation: AAH17425.1.
    CCDSiCCDS1762.1. [Q9H477-1]
    RefSeqiNP_001274509.1. NM_001287580.1.
    NP_071411.1. NM_022128.2. [Q9H477-1]
    UniGeneiHs.11916.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2FV7X-ray2.10A/B11-322[»]
    5BYCX-ray1.95A/B1-322[»]
    5BYDX-ray2.10A/B1-322[»]
    5BYEX-ray1.75A/B1-322[»]
    5BYFX-ray2.00A/B1-322[»]
    5C3YX-ray2.60A/B/C/D/E/F/G/H/I/J/K/L1-322[»]
    5C3ZX-ray1.90A/B1-322[»]
    5C40X-ray1.50A/B1-322[»]
    5C41X-ray1.95A/B/C/D1-322[»]
    ProteinModelPortaliQ9H477.
    SMRiQ9H477.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi122046. 10 interactors.
    IntActiQ9H477. 6 interactors.
    STRINGi9606.ENSP00000306817.

    PTM databases

    iPTMnetiQ9H477.
    PhosphoSitePlusiQ9H477.

    Polymorphism and mutation databases

    DMDMi20139730.

    Proteomic databases

    EPDiQ9H477.
    MaxQBiQ9H477.
    PaxDbiQ9H477.
    PeptideAtlasiQ9H477.
    PRIDEiQ9H477.

    Protocols and materials databases

    DNASUi64080.
    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsembliENST00000302188; ENSP00000306817; ENSG00000171174. [Q9H477-1]
    GeneIDi64080.
    KEGGihsa:64080.
    UCSCiuc002rlo.3. human. [Q9H477-1]

    Organism-specific databases

    CTDi64080.
    DisGeNETi64080.
    GeneCardsiRBKS.
    HGNCiHGNC:30325. RBKS.
    HPAiHPA019725.
    HPA028285.
    MIMi611132. gene.
    neXtProtiNX_Q9H477.
    OpenTargetsiENSG00000171174.
    PharmGKBiPA134951602.
    GenAtlasiSearch...

    Phylogenomic databases

    eggNOGiKOG2855. Eukaryota.
    COG0524. LUCA.
    GeneTreeiENSGT00390000005743.
    HOGENOMiHOG000235950.
    HOVERGENiHBG018350.
    InParanoidiQ9H477.
    KOiK00852.
    OMAiNDSPFVA.
    OrthoDBiEOG091G08OZ.
    PhylomeDBiQ9H477.
    TreeFamiTF105770.

    Enzyme and pathway databases

    UniPathwayiUPA00916; UER00889.
    BioCyciZFISH:HS10260-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiQ9H477.
    GenomeRNAii64080.
    PROiQ9H477.
    SOURCEiSearch...

    Gene expression databases

    BgeeiENSG00000171174.
    ExpressionAtlasiQ9H477. baseline and differential.
    GenevisibleiQ9H477. HS.

    Family and domain databases

    CDDicd01174. ribokinase. 1 hit.
    Gene3Di3.40.1190.20. 1 hit.
    HAMAPiMF_01987. Ribokinase. 1 hit.
    InterProiIPR002173. Carboh/pur_kinase_PfkB_CS.
    IPR011877. D_ribokin.
    IPR011611. PfkB_dom.
    IPR002139. Ribo/fructo_kinase.
    IPR029056. Ribokinase-like.
    [Graphical view]
    PfamiPF00294. PfkB. 1 hit.
    [Graphical view]
    PRINTSiPR00990. RIBOKINASE.
    SUPFAMiSSF53613. SSF53613. 1 hit.
    TIGRFAMsiTIGR02152. D_ribokin_bact. 1 hit.
    PROSITEiPS00584. PFKB_KINASES_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiRBSK_HUMAN
    AccessioniPrimary (citable) accession number: Q9H477
    Secondary accession number(s): A9UK04, B4DV96
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 23, 2002
    Last sequence update: March 1, 2001
    Last modified: November 2, 2016
    This is version 136 of the entry and version 1 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

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Human chromosome 2
      Human chromosome 2: entries, gene names and cross-references to MIM
    2. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    3. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    4. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    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.