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Protein

Ribokinase

Gene

RBKS

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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

    Keywordsi

    Molecular functionKinase, Transferase
    Biological processCarbohydrate metabolism
    LigandATP-binding, Magnesium, Metal-binding, Nucleotide-binding, Potassium

    Enzyme and pathway databases

    ReactomeiR-HSA-71336 Pentose phosphate pathway (hexose monophosphate shunt)
    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

    EuPathDBiHostDB:ENSG00000171174.13
    HGNCiHGNC:30325 RBKS
    MIMi611132 gene
    neXtProtiNX_Q9H477

    Subcellular locationi

    Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

    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

    Show more details

    Protein-protein interaction databases

    BioGridi122046, 11 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
    OMAiNADHVIS
    OrthoDBiEOG091G08OZ
    PhylomeDBiQ9H477
    TreeFamiTF105770

    Family and domain databases

    CDDicd01174 ribokinase, 1 hit
    Gene3Di3.40.1190.20, 1 hit
    HAMAPiMF_01987 Ribokinase, 1 hit
    InterProiView protein in InterPro
    IPR002173 Carboh/pur_kinase_PfkB_CS
    IPR011877 D_ribokin
    IPR011611 PfkB_dom
    IPR002139 Ribo/fructo_kinase
    IPR029056 Ribokinase-like
    PfamiView protein in Pfam
    PF00294 PfkB, 1 hit
    PRINTSiPR00990 RIBOKINASE
    SUPFAMiSSF53613 SSF53613, 1 hit
    TIGRFAMsiTIGR02152 D_ribokin_bact, 1 hit
    PROSITEiView protein in PROSITE
    PS00584 PFKB_KINASES_2, 1 hit

    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

    Similar proteinsi

    Entry informationi

    Entry nameiRBSK_HUMAN
    AccessioniPrimary (citable) accession number: Q9H477
    Secondary accession number(s): A9UK04, B4DV96
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 23, 2002
    Last sequence update: March 1, 2001
    Last modified: May 23, 2018
    This is version 145 of the entry and version 1 of the sequence. See 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

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