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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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei154 – 1541SubstrateUniRule annotationBy similarity
    Binding sitei199 – 1991ATPUniRule annotation1 Publication
    Binding sitei256 – 2561ATPUniRule annotation1 Publication
    Metal bindingi263 – 2631PotassiumUniRule annotation1 Publication
    Metal bindingi265 – 2651Potassium; via carbonyl oxygenUniRule annotationBy similarity
    Active sitei269 – 2691Proton acceptorUniRule annotationBy similarity
    Binding sitei269 – 2691SubstrateUniRule annotationBy similarity
    Binding sitei295 – 2951ATPUniRule annotation1 Publication
    Metal bindingi301 – 3011Potassium; via carbonyl oxygenUniRule annotation1 Publication
    Metal bindingi304 – 3041Potassium; via carbonyl oxygenUniRule annotation1 Publication
    Metal bindingi306 – 3061Potassium; via carbonyl oxygenUniRule annotationBy similarity
    Metal bindingi310 – 3101PotassiumUniRule annotation1 Publication

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi235 – 2406ATPUniRule annotation1 Publication
    Nucleotide bindingi268 – 2692ATPUniRule annotation1 Publication

    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

    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

    PharmGKBiPA134951602.

    Polymorphism and mutation databases

    DMDMi20139730.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 322322RibokinasePRO_0000080092Add
    BLAST

    Proteomic databases

    EPDiQ9H477.
    MaxQBiQ9H477.
    PaxDbiQ9H477.
    PeptideAtlasiQ9H477.
    PRIDEiQ9H477.

    PTM databases

    iPTMnetiQ9H477.
    PhosphoSiteiQ9H477.

    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 interactions.
    IntActiQ9H477. 6 interactions.
    STRINGi9606.ENSP00000306817.

    Structurei

    Secondary structure

    1
    322
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi17 – 215Combined sources
    Beta strandi25 – 317Combined sources
    Beta strandi45 – 528Combined sources
    Helixi54 – 6411Combined sources
    Beta strandi69 – 7810Combined sources
    Helixi79 – 8911Combined sources
    Turni90 – 923Combined sources
    Beta strandi98 – 1047Combined sources
    Beta strandi107 – 1137Combined sources
    Beta strandi119 – 1246Combined sources
    Helixi126 – 1305Combined sources
    Helixi133 – 1386Combined sources
    Helixi140 – 1456Combined sources
    Beta strandi147 – 1515Combined sources
    Beta strandi153 – 1553Combined sources
    Helixi157 – 16913Combined sources
    Beta strandi173 – 1764Combined sources
    Helixi188 – 1914Combined sources
    Beta strandi194 – 1996Combined sources
    Helixi200 – 2078Combined sources
    Helixi214 – 22512Combined sources
    Turni226 – 2283Combined sources
    Beta strandi230 – 2356Combined sources
    Helixi237 – 2393Combined sources
    Beta strandi241 – 2477Combined sources
    Beta strandi252 – 2543Combined sources
    Helixi267 – 28115Combined sources
    Helixi287 – 30216Combined sources
    Beta strandi304 – 3063Combined sources
    Helixi307 – 3104Combined sources
    Helixi314 – 3163Combined sources
    Helixi319 – 3213Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    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. Positions 15-322.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9H477.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni25 – 273Substrate bindingUniRule annotationBy similarity
    Regioni53 – 575Substrate bindingUniRule annotationBy similarity

    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

    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)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti101 – 1011T → A in AAT64917 (Ref. 2) Curated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei266 – 32257GAGDS…PLTLF → CRPGSRPKSEAASVKKQKHY K in isoform 2. 1 PublicationVSP_054380Add
    BLAST

    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
    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. Positions 15-322.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi122046. 10 interactions.
    IntActiQ9H477. 6 interactions.
    STRINGi9606.ENSP00000306817.

    PTM databases

    iPTMnetiQ9H477.
    PhosphoSiteiQ9H477.

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

    Phylogenomic databases

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

    Enzyme and pathway databases

    UniPathwayiUPA00916; UER00889.

    Miscellaneous databases

    EvolutionaryTraceiQ9H477.
    GenomeRNAii64080.
    PROiQ9H477.
    SOURCEiSearch...

    Gene expression databases

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

    Family and domain databases

    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: September 7, 2016
    This is version 134 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.