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Protein

Xylulose kinase

Gene

XYLB

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

Functioni

Phosphorylates D-xylulose to produce D-xylulose 5-phosphate, a molecule that may play an important role in the regulation of glucose metabolism and lipogenesis.1 Publication

Catalytic activityi

ATP + D-xylulose = ADP + D-xylulose 5-phosphate.1 Publication

Kineticsi

  1. KM=24 µM for D-xylulose1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei99 – 991Substrate
    Binding sitei170 – 1701Substrate
    Binding sitei280 – 2801Substrate
    Binding sitei281 – 2811Substrate
    Binding sitei355 – 3551ATP
    Binding sitei445 – 4451ATP

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi441 – 4422ATP

    GO - Molecular functioni

    • ATP binding Source: UniProtKB-KW
    • xylulokinase activity Source: UniProtKB

    GO - Biological processi

    • carbohydrate metabolic process Source: ProtInc
    • carbohydrate phosphorylation Source: GOC
    • D-xylose metabolic process Source: UniProtKB-KW
    • generation of precursor metabolites and energy Source: ProtInc
    • xylulose catabolic process Source: BHF-UCL
    • xylulose metabolic process Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Kinase, Transferase

    Keywords - Biological processi

    Carbohydrate metabolism, Xylose metabolism

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BRENDAi2.7.1.17. 2681.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Xylulose kinase (EC:2.7.1.17)
    Short name:
    Xylulokinase
    Gene namesi
    Name:XYLB
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640 Componenti: Chromosome 3

    Organism-specific databases

    HGNCiHGNC:12839. XYLB.

    Subcellular locationi

    GO - Cellular componenti

    • cytoplasm Source: GO_Central
    • extracellular exosome Source: UniProtKB
    Complete GO annotation...

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA37430.

    Polymorphism and mutation databases

    BioMutaiXYLB.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 536536Xylulose kinasePRO_0000230985Add
    BLAST

    Proteomic databases

    MaxQBiO75191.
    PaxDbiO75191.
    PRIDEiO75191.

    PTM databases

    PhosphoSiteiO75191.

    Expressioni

    Gene expression databases

    BgeeiO75191.
    CleanExiHS_XYLB.
    ExpressionAtlasiO75191. baseline and differential.
    GenevisibleiO75191. HS.

    Organism-specific databases

    HPAiHPA037863.
    HPA038415.

    Interactioni

    Subunit structurei

    Monomer.1 Publication

    Protein-protein interaction databases

    BioGridi115268. 1 interaction.
    STRINGi9606.ENSP00000207870.

    Structurei

    Secondary structure

    1
    536
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi9 – 157Combined sources
    Beta strandi17 – 2610Combined sources
    Beta strandi31 – 388Combined sources
    Helixi39 – 424Combined sources
    Helixi44 – 463Combined sources
    Beta strandi52 – 543Combined sources
    Beta strandi61 – 644Combined sources
    Helixi65 – 8117Combined sources
    Helixi86 – 883Combined sources
    Beta strandi89 – 968Combined sources
    Beta strandi101 – 1055Combined sources
    Helixi108 – 1136Combined sources
    Helixi121 – 1255Combined sources
    Beta strandi132 – 1354Combined sources
    Helixi143 – 15311Combined sources
    Helixi156 – 1638Combined sources
    Helixi172 – 18211Combined sources
    Helixi184 – 1885Combined sources
    Beta strandi190 – 1956Combined sources
    Helixi196 – 20510Combined sources
    Helixi213 – 2164Combined sources
    Beta strandi218 – 2203Combined sources
    Turni224 – 2274Combined sources
    Helixi231 – 2377Combined sources
    Helixi241 – 2455Combined sources
    Beta strandi254 – 2574Combined sources
    Helixi260 – 2667Combined sources
    Beta strandi273 – 2753Combined sources
    Helixi280 – 2878Combined sources
    Beta strandi295 – 31117Combined sources
    Beta strandi316 – 3238Combined sources
    Beta strandi326 – 33914Combined sources
    Helixi340 – 35011Combined sources
    Helixi355 – 3639Combined sources
    Helixi369 – 3713Combined sources
    Beta strandi373 – 3797Combined sources
    Beta strandi382 – 3843Combined sources
    Beta strandi388 – 3925Combined sources
    Beta strandi398 – 4003Combined sources
    Helixi404 – 42522Combined sources
    Beta strandi436 – 4405Combined sources
    Helixi441 – 4444Combined sources
    Helixi446 – 45611Combined sources
    Beta strandi460 – 4623Combined sources
    Helixi468 – 48114Combined sources
    Helixi484 – 4863Combined sources
    Helixi489 – 4935Combined sources
    Beta strandi500 – 5034Combined sources
    Helixi509 – 53022Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4BC2X-ray1.97A/B/C1-536[»]
    4BC3X-ray1.68A/B/C1-536[»]
    4BC4X-ray1.79A/B/C1-536[»]
    4BC5X-ray1.98A/B/C1-536[»]
    ProteinModelPortaliO75191.
    SMRiO75191. Positions 6-531.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the FGGY kinase family.Curated

    Phylogenomic databases

    eggNOGiCOG1070.
    GeneTreeiENSGT00390000010821.
    HOGENOMiHOG000174850.
    HOVERGENiHBG053124.
    InParanoidiO75191.
    KOiK00854.
    OMAiGSYSPID.
    PhylomeDBiO75191.
    TreeFamiTF313643.

    Family and domain databases

    InterProiIPR018485. Carb_kinase_FGGY_C.
    IPR018484. Carb_kinase_FGGY_N.
    [Graphical view]
    PfamiPF02782. FGGY_C. 1 hit.
    PF00370. FGGY_N. 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: O75191-1) [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
    MAEHAPRRCC LGWDFSTQQV KVVAVDAELN VFYEESVHFD RDLPEFGTQG
    60 70 80 90 100
    GVHVHKDGLT VTSPVLMWVQ ALDIILEKMK ASGFDFSQVL ALSGAGQQHG
    110 120 130 140 150
    SIYWKAGAQQ ALTSLSPDLR LHQQLQDCFS ISDCPVWMDS STTAQCRQLE
    160 170 180 190 200
    AAVGGAQALS CLTGSRAYER FTGNQIAKIY QQNPEAYSHT ERISLVSSFA
    210 220 230 240 250
    ASLFLGSYSP IDYSDGSGMN LLQIQDKVWS QACLGACAPH LEEKLSPPVP
    260 270 280 290 300
    SCSVVGAISS YYVQRYGFPP GCKVVAFTGD NPASLAGMRL EEGDIAVSLG
    310 320 330 340 350
    TSDTLFLWLQ EPMPALEGHI FCNPVDSQHY MALLCFKNGS LMREKIRNES
    360 370 380 390 400
    VSRSWSDFSK ALQSTEMGNG GNLGFYFDVM EITPEIIGRH RFNTENHKVA
    410 420 430 440 450
    AFPGDVEVRA LIEGQFMAKR IHAEGLGYRV MSKTKILATG GASHNREILQ
    460 470 480 490 500
    VLADVFDAPV YVIDTANSAC VGSAYRAFHG LAGGTDVPFS EVVKLAPNPR
    510 520 530
    LAATPSPGAS QVYEALLPQY AKLEQRILSQ TRGPPE
    Length:536
    Mass (Da):58,382
    Last modified:May 5, 2009 - v3
    Checksum:iE2FC1C45308D71A8
    GO
    Isoform 2 (identifier: O75191-2) [UniParc]FASTAAdd to basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-137: Missing.

    Note: No experimental confirmation available.
    Show »
    Length:399
    Mass (Da):43,182
    Checksum:iBF7C28142BABD317
    GO

    Sequence cautioni

    The sequence BAA31527.1 differs from that shown.Probable cloning artifact.Curated

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti85 – 851D → E.3 Publications
    Corresponds to variant rs17118 [ dbSNP | Ensembl ].
    VAR_055151
    Natural varianti133 – 1331D → N.
    Corresponds to variant rs2234610 [ dbSNP | Ensembl ].
    VAR_055152
    Natural varianti139 – 1391D → E.
    Corresponds to variant rs151611 [ dbSNP | Ensembl ].
    VAR_055153
    Natural varianti262 – 2621Y → N.1 Publication
    Corresponds to variant rs196380 [ dbSNP | Ensembl ].
    VAR_055154
    Natural varianti348 – 3481N → D.
    Corresponds to variant rs2234622 [ dbSNP | Ensembl ].
    VAR_055155

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei1 – 137137Missing in isoform 2. 1 PublicationVSP_055522Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AK293325 mRNA. Translation: BAG56843.1.
    AK314386 mRNA. Translation: BAG37011.1.
    AP006191 Genomic DNA. No translation available.
    AP006193 Genomic DNA. No translation available.
    CH471055 Genomic DNA. Translation: EAW64532.1.
    BC137076 mRNA. Translation: AAI37077.1.
    BC137080 mRNA. Translation: AAI37081.1.
    AB015046 mRNA. Translation: BAA31527.1. Sequence problems.
    CCDSiCCDS2678.1. [O75191-1]
    RefSeqiNP_005099.2. NM_005108.3. [O75191-1]
    UniGeneiHs.659985.

    Genome annotation databases

    EnsembliENST00000207870; ENSP00000207870; ENSG00000093217.
    GeneIDi9942.
    KEGGihsa:9942.
    UCSCiuc003cic.2. human. [O75191-1]

    Keywords - Coding sequence diversityi

    Alternative splicing, Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AK293325 mRNA. Translation: BAG56843.1.
    AK314386 mRNA. Translation: BAG37011.1.
    AP006191 Genomic DNA. No translation available.
    AP006193 Genomic DNA. No translation available.
    CH471055 Genomic DNA. Translation: EAW64532.1.
    BC137076 mRNA. Translation: AAI37077.1.
    BC137080 mRNA. Translation: AAI37081.1.
    AB015046 mRNA. Translation: BAA31527.1. Sequence problems.
    CCDSiCCDS2678.1. [O75191-1]
    RefSeqiNP_005099.2. NM_005108.3. [O75191-1]
    UniGeneiHs.659985.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4BC2X-ray1.97A/B/C1-536[»]
    4BC3X-ray1.68A/B/C1-536[»]
    4BC4X-ray1.79A/B/C1-536[»]
    4BC5X-ray1.98A/B/C1-536[»]
    ProteinModelPortaliO75191.
    SMRiO75191. Positions 6-531.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi115268. 1 interaction.
    STRINGi9606.ENSP00000207870.

    PTM databases

    PhosphoSiteiO75191.

    Polymorphism and mutation databases

    BioMutaiXYLB.

    Proteomic databases

    MaxQBiO75191.
    PaxDbiO75191.
    PRIDEiO75191.

    Protocols and materials databases

    DNASUi9942.
    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsembliENST00000207870; ENSP00000207870; ENSG00000093217.
    GeneIDi9942.
    KEGGihsa:9942.
    UCSCiuc003cic.2. human. [O75191-1]

    Organism-specific databases

    CTDi9942.
    GeneCardsiGC03P038363.
    H-InvDBHIX0003180.
    HGNCiHGNC:12839. XYLB.
    HPAiHPA037863.
    HPA038415.
    MIMi604049. gene.
    neXtProtiNX_O75191.
    PharmGKBiPA37430.
    GenAtlasiSearch...

    Phylogenomic databases

    eggNOGiCOG1070.
    GeneTreeiENSGT00390000010821.
    HOGENOMiHOG000174850.
    HOVERGENiHBG053124.
    InParanoidiO75191.
    KOiK00854.
    OMAiGSYSPID.
    PhylomeDBiO75191.
    TreeFamiTF313643.

    Enzyme and pathway databases

    BRENDAi2.7.1.17. 2681.

    Miscellaneous databases

    GenomeRNAii9942.
    NextBioi35471022.
    PROiO75191.
    SOURCEiSearch...

    Gene expression databases

    BgeeiO75191.
    CleanExiHS_XYLB.
    ExpressionAtlasiO75191. baseline and differential.
    GenevisibleiO75191. HS.

    Family and domain databases

    InterProiIPR018485. Carb_kinase_FGGY_C.
    IPR018484. Carb_kinase_FGGY_N.
    [Graphical view]
    PfamiPF02782. FGGY_C. 1 hit.
    PF00370. FGGY_N. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
      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.
      Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2), VARIANT GLU-85.
      Tissue: Kidney and Mammary gland.
    2. "The DNA sequence, annotation and analysis of human chromosome 3."
      Muzny D.M., Scherer S.E., Kaul R., Wang J., Yu J., Sudbrak R., Buhay C.J., Chen R., Cree A., Ding Y., Dugan-Rocha S., Gill R., Gunaratne P., Harris R.A., Hawes A.C., Hernandez J., Hodgson A.V., Hume J.
      , Jackson A., Khan Z.M., Kovar-Smith C., Lewis L.R., Lozado R.J., Metzker M.L., Milosavljevic A., Miner G.R., Morgan M.B., Nazareth L.V., Scott G., Sodergren E., Song X.-Z., Steffen D., Wei S., Wheeler D.A., Wright M.W., Worley K.C., Yuan Y., Zhang Z., Adams C.Q., Ansari-Lari M.A., Ayele M., Brown M.J., Chen G., Chen Z., Clendenning J., Clerc-Blankenburg K.P., Chen R., Chen Z., Davis C., Delgado O., Dinh H.H., Dong W., Draper H., Ernst S., Fu G., Gonzalez-Garay M.L., Garcia D.K., Gillett W., Gu J., Hao B., Haugen E., Havlak P., He X., Hennig S., Hu S., Huang W., Jackson L.R., Jacob L.S., Kelly S.H., Kube M., Levy R., Li Z., Liu B., Liu J., Liu W., Lu J., Maheshwari M., Nguyen B.-V., Okwuonu G.O., Palmeiri A., Pasternak S., Perez L.M., Phelps K.A., Plopper F.J., Qiang B., Raymond C., Rodriguez R., Saenphimmachak C., Santibanez J., Shen H., Shen Y., Subramanian S., Tabor P.E., Verduzco D., Waldron L., Wang J., Wang J., Wang Q., Williams G.A., Wong G.K.-S., Yao Z., Zhang J., Zhang X., Zhao G., Zhou J., Zhou Y., Nelson D., Lehrach H., Reinhardt R., Naylor S.L., Yang H., Olson M., Weinstock G., Gibbs R.A.
      Nature 440:1194-1198(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], VARIANT GLU-85.
    4. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
      Tissue: Lung and Testis.
    5. "Genomic structure of a novel human gene (XYLB) on chromosome 3p22-->p21.3 encoding a xylulokinase-like protein."
      Tamari M., Daigo Y., Ishikawa S., Nakamura Y.
      Cytogenet. Cell Genet. 82:101-104(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1-512 (ISOFORM 1), VARIANTS GLU-85 AND ASN-262.
      Tissue: Liver.
    6. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    7. "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome."
      Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L., Ye M., Zou H.
      J. Proteomics 96:253-262(2014) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Liver.
    8. "Structure and function of human xylulokinase, an enzyme with important roles in carbohydrate metabolism."
      Bunker R.D., Bulloch E.M., Dickson J.M., Loomes K.M., Baker E.N.
      J. Biol. Chem. 288:1643-1652(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.68 ANGSTROMS) IN COMPLEX WITH D-XYLULOSE AND ADP, CATALYTIC ACTIVITY, FUNCTION, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES.

    Entry informationi

    Entry nameiXYLB_HUMAN
    AccessioniPrimary (citable) accession number: O75191
    Secondary accession number(s): B2RAW4, B4DDT2, B9EH64
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 4, 2006
    Last sequence update: May 5, 2009
    Last modified: July 22, 2015
    This is version 101 of the entry and version 3 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 3
      Human chromosome 3: 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. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    6. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3

    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 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.