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Protein

Xanthine phosphoribosyltransferase

Gene

xpt

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Converts the preformed base xanthine, a product of nucleic acid breakdown, to xanthosine 5'-monophosphate (XMP), so that it can be reused for RNA or DNA synthesis.

Catalytic activityi

XMP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + xanthine.

Kineticsi

  1. KM=2.2 µM for xanthine1 Publication
  2. KM=281 µM for guanine1 Publication
  3. KM=1250 µM for hypoxanthine1 Publication

    pH dependencei

    Optimum pH is 6-9.1 Publication

    Pathwayi: XMP biosynthesis via salvage pathway

    This protein is involved in step 1 of the subpathway that synthesizes XMP from xanthine.
    Proteins known to be involved in this subpathway in this organism are:
    1. Xanthine phosphoribosyltransferase (xpt)
    This subpathway is part of the pathway XMP biosynthesis via salvage pathway, which is itself part of Purine metabolism.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes XMP from xanthine, the pathway XMP biosynthesis via salvage pathway and in Purine metabolism.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei20 – 201Xanthine; via amide nitrogen and carbonyl oxygen
    Binding sitei27 – 271Xanthine
    Binding sitei156 – 1561Xanthine

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Glycosyltransferase, Transferase

    Keywords - Biological processi

    Purine salvage

    Enzyme and pathway databases

    BioCyciBSUB:BSU22070-MONOMER.
    BRENDAi2.4.2.22. 658.
    UniPathwayiUPA00602; UER00658.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Xanthine phosphoribosyltransferase (EC:2.4.2.22)
    Short name:
    XPRTase
    Gene namesi
    Name:xpt
    Ordered Locus Names:BSU22070
    OrganismiBacillus subtilis (strain 168)
    Taxonomic identifieri224308 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    Proteomesi
    • UP000001570 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 194194Xanthine phosphoribosyltransferasePRO_0000139697Add
    BLAST

    Proteomic databases

    PaxDbiP42085.

    Expressioni

    Inductioni

    Repressed during growth on purines as a nitrogen source.1 Publication

    Interactioni

    Subunit structurei

    Homodimer.2 Publications

    Protein-protein interaction databases

    STRINGi224308.Bsubs1_010100012151.

    Structurei

    Secondary structure

    194
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi1 – 1111Combined sources
    Beta strandi13 – 153Combined sources
    Turni16 – 183Combined sources
    Beta strandi19 – 213Combined sources
    Turni23 – 264Combined sources
    Beta strandi27 – 304Combined sources
    Helixi32 – 4514Combined sources
    Turni46 – 505Combined sources
    Beta strandi53 – 575Combined sources
    Turni58 – 614Combined sources
    Helixi62 – 7211Combined sources
    Beta strandi76 – 827Combined sources
    Beta strandi89 – 9810Combined sources
    Turni99 – 1024Combined sources
    Beta strandi103 – 1108Combined sources
    Helixi111 – 1133Combined sources
    Beta strandi119 – 12911Combined sources
    Helixi131 – 14212Combined sources
    Beta strandi146 – 15611Combined sources
    Helixi161 – 1677Combined sources
    Beta strandi172 – 1809Combined sources
    Turni182 – 1843Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1Y0BX-ray1.80A/B/C/D1-194[»]
    2FXVX-ray2.05A/B1-194[»]
    ProteinModelPortaliP42085.
    SMRiP42085. Positions 1-191.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP42085.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni128 – 13255-phospho-alpha-D-ribose 1-diphosphate binding

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4108UPS. Bacteria.
    COG0503. LUCA.
    HOGENOMiHOG000036777.
    InParanoidiP42085.
    KOiK03816.
    OMAiHQIDPEL.
    OrthoDBiEOG6GTZNX.
    PhylomeDBiP42085.

    Family and domain databases

    Gene3Di3.40.50.2020. 1 hit.
    HAMAPiMF_01184. XPRTase.
    InterProiIPR000836. PRibTrfase_dom.
    IPR029057. PRTase-like.
    IPR010079. Xanthine_PRibTrfase.
    [Graphical view]
    PfamiPF00156. Pribosyltran. 1 hit.
    [Graphical view]
    SUPFAMiSSF53271. SSF53271. 1 hit.
    TIGRFAMsiTIGR01744. XPRTase. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P42085-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MEALKRKIEE EGVVLSDQVL KVDSFLNHQI DPLLMQRIGD EFASRFAKDG
    60 70 80 90 100
    ITKIVTIESS GIAPAVMTGL KLGVPVVFAR KHKSLTLTDN LLTASVYSFT
    110 120 130 140 150
    KQTESQIAVS GTHLSDQDHV LIIDDFLANG QAAHGLVSIV KQAGASIAGI
    160 170 180 190
    GIVIEKSFQP GRDELVKLGY RVESLARIQS LEEGKVSFVQ EVHS
    Length:194
    Mass (Da):21,038
    Last modified:November 1, 1995 - v1
    Checksum:i86DE53F467A52EDE
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X83878 Genomic DNA. Translation: CAA58758.1.
    L77246 Genomic DNA. Translation: AAA96611.1.
    AL009126 Genomic DNA. Translation: CAB14124.1.
    PIRiS51309.
    RefSeqiNP_390089.1. NC_000964.3.
    WP_003230744.1. NZ_JNCM01000036.1.

    Genome annotation databases

    EnsemblBacteriaiCAB14124; CAB14124; BSU22070.
    GeneIDi939064.
    KEGGibsu:BSU22070.
    PATRICi18976221. VBIBacSub10457_2301.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X83878 Genomic DNA. Translation: CAA58758.1.
    L77246 Genomic DNA. Translation: AAA96611.1.
    AL009126 Genomic DNA. Translation: CAB14124.1.
    PIRiS51309.
    RefSeqiNP_390089.1. NC_000964.3.
    WP_003230744.1. NZ_JNCM01000036.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1Y0BX-ray1.80A/B/C/D1-194[»]
    2FXVX-ray2.05A/B1-194[»]
    ProteinModelPortaliP42085.
    SMRiP42085. Positions 1-191.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi224308.Bsubs1_010100012151.

    Proteomic databases

    PaxDbiP42085.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCAB14124; CAB14124; BSU22070.
    GeneIDi939064.
    KEGGibsu:BSU22070.
    PATRICi18976221. VBIBacSub10457_2301.

    Phylogenomic databases

    eggNOGiENOG4108UPS. Bacteria.
    COG0503. LUCA.
    HOGENOMiHOG000036777.
    InParanoidiP42085.
    KOiK03816.
    OMAiHQIDPEL.
    OrthoDBiEOG6GTZNX.
    PhylomeDBiP42085.

    Enzyme and pathway databases

    UniPathwayiUPA00602; UER00658.
    BioCyciBSUB:BSU22070-MONOMER.
    BRENDAi2.4.2.22. 658.

    Miscellaneous databases

    EvolutionaryTraceiP42085.

    Family and domain databases

    Gene3Di3.40.50.2020. 1 hit.
    HAMAPiMF_01184. XPRTase.
    InterProiIPR000836. PRibTrfase_dom.
    IPR029057. PRTase-like.
    IPR010079. Xanthine_PRibTrfase.
    [Graphical view]
    PfamiPF00156. Pribosyltran. 1 hit.
    [Graphical view]
    SUPFAMiSSF53271. SSF53271. 1 hit.
    TIGRFAMsiTIGR01744. XPRTase. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Xanthine metabolism in Bacillus subtilis: characterization of the xpt-pbuX operon and evidence for purine- and nitrogen-controlled expression of genes involved in xanthine salvage and catabolism."
      Christiansen L.C., Schou S., Nygaard P., Saxild H.H.
      J. Bacteriol. 179:2540-2550(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], INDUCTION.
      Strain: 168.
    2. "Organization of the Bacillus subtilis 168 chromosome between kdg and the attachment site of the SP beta prophage: use of long accurate PCR and yeast artificial chromosomes for sequencing."
      Capuano V., Galleron N., Pujic P., Sorokin A., Ehrlich S.D.
      Microbiology 142:3005-3015(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: 168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB 3610 / VKM B-501.
    3. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
      Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
      , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
      Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: 168.
    4. "Crystal structure of xanthine phosphoribosyltransferase from Bacillus subtilis."
      Midwest center for structural genomics (MCSG)
      Submitted (FEB-2005) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH GUANINE TETRAPHOSPHATE.
    5. "The extraordinary specificity of xanthine phosphoribosyltransferase from Bacillus subtilis elucidated by reaction kinetics, ligand binding, and crystallography."
      Arent S., Kadziola A., Larsen S., Neuhard J., Jensen K.F.
      Biochemistry 45:6615-6627(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) IN COMPLEX WITH GMP, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES.
      Strain: 168.

    Entry informationi

    Entry nameiXPT_BACSU
    AccessioniPrimary (citable) accession number: P42085
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1995
    Last sequence update: November 1, 1995
    Last modified: February 17, 2016
    This is version 115 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Highly specific for xanthine, with a strong discrimination against hypoxanthine and guanine as substrates.

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Bacillus subtilis
      Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. 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.