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P77836

- PDP_GEOSE

UniProt

P77836 - PDP_GEOSE

Protein

Pyrimidine-nucleoside phosphorylase

Gene

pdp

Organism
Geobacillus stearothermophilus (Bacillus stearothermophilus)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 97 (01 Oct 2014)
      Sequence version 1 (01 Feb 1997)
      Previous versions | rss
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    Functioni

    Catalytic activityi

    Uridine + phosphate = uracil + alpha-D-ribose 1-phosphate.
    Thymidine + phosphate = thymine + 2'-deoxy-alpha-D-ribose 1-phosphate.
    2'-deoxyuridine + phosphate = uracil + 2'-deoxy-alpha-D-ribose 1-phosphate.

    Cofactori

    Binds 1 potassium ion per subunit.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi88 – 881Potassium; via carbonyl oxygen
    Metal bindingi90 – 901Potassium
    Metal bindingi243 – 2431Potassium; via carbonyl oxygen
    Metal bindingi246 – 2461Potassium; via carbonyl oxygen
    Metal bindingi255 – 2551Potassium

    GO - Molecular functioni

    1. metal ion binding Source: UniProtKB-KW
    2. phosphorylase activity Source: InterPro
    3. pyrimidine-nucleoside phosphorylase activity Source: UniProtKB-EC

    GO - Biological processi

    1. pyrimidine nucleobase metabolic process Source: InterPro
    2. pyrimidine nucleoside metabolic process Source: InterPro

    Keywords - Molecular functioni

    Glycosyltransferase, Transferase

    Keywords - Ligandi

    Metal-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-17881.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Pyrimidine-nucleoside phosphorylase (EC:2.4.2.2)
    Short name:
    PYNP
    Gene namesi
    Name:pdp
    Synonyms:pyn
    OrganismiGeobacillus stearothermophilus (Bacillus stearothermophilus)
    Taxonomic identifieri1422 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeGeobacillus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 433433Pyrimidine-nucleoside phosphorylasePRO_0000059083Add
    BLAST

    Proteomic databases

    PRIDEiP77836.

    Interactioni

    Subunit structurei

    Homodimer.

    Structurei

    Secondary structure

    1
    433
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi3 – 119
    Helixi18 – 2912
    Helixi35 – 4814
    Helixi52 – 6413
    Beta strandi79 – 835
    Helixi91 – 10010
    Turni101 – 1033
    Beta strandi106 – 1105
    Helixi120 – 1245
    Helixi136 – 14611
    Beta strandi147 – 1526
    Helixi159 – 17012
    Helixi177 – 19115
    Beta strandi194 – 20310
    Helixi211 – 22717
    Beta strandi231 – 2388
    Beta strandi243 – 2497
    Helixi250 – 26011
    Helixi266 – 28217
    Beta strandi285 – 2884
    Helixi289 – 30214
    Helixi304 – 31512
    Helixi320 – 3223
    Helixi326 – 3283
    Beta strandi333 – 3397
    Beta strandi341 – 3499
    Helixi351 – 36111
    Beta strandi377 – 3815
    Beta strandi393 – 40210
    Helixi405 – 4128
    Beta strandi415 – 4206
    Beta strandi427 – 4326

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1BRWX-ray2.10A/B1-432[»]
    ProteinModelPortaliP77836.
    SMRiP77836. Positions 1-432.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP77836.

    Family & Domainsi

    Sequence similaritiesi

    Family and domain databases

    Gene3Di3.40.1030.10. 1 hit.
    3.90.1170.30. 1 hit.
    InterProiIPR000312. Glycosyl_Trfase_fam3.
    IPR017459. Glycosyl_Trfase_fam3_N_dom.
    IPR013102. PYNP_C.
    IPR018090. Pyrmidine_PPas_bac/euk.
    IPR000053. Pyrmidine_PPase.
    IPR017872. Pyrmidine_PPase_CS.
    [Graphical view]
    PANTHERiPTHR10515. PTHR10515. 1 hit.
    PfamiPF02885. Glycos_trans_3N. 1 hit.
    PF00591. Glycos_transf_3. 1 hit.
    PF07831. PYNP_C. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000478. TP_PyNP. 1 hit.
    SMARTiSM00941. PYNP_C. 1 hit.
    [Graphical view]
    SUPFAMiSSF47648. SSF47648. 1 hit.
    SSF52418. SSF52418. 1 hit.
    SSF54680. SSF54680. 1 hit.
    TIGRFAMsiTIGR02644. Y_phosphoryl. 1 hit.
    PROSITEiPS00647. THYMID_PHOSPHORYLASE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P77836-1 [UniParc]FASTAAdd to Basket

    « Hide

    MRMVDLIEKK RDGHALTKEE IQFIIEGYTK GDIPDYQMSA LAMAIFFRGM    50
    NEEETAELTM AMVHSGDTID LSRIEGIKVD KHSTGGVGDT TTLVLGPLVA 100
    SVGVPVAKMS GRGLGHTGGT IDKLESVPGF HVEITNDEFI DLVNKNKIAV 150
    VGQSGNLTPA DKKLYALRDV TATVNSIPLI ASSIMSKKIA AGADAIVLDV 200
    KTGVGAFMKD LNDAKALAKA MVDIGNRVGR KTMAIISDMS QPLGYAIGNA 250
    LEVKEAIDTL KGEGPEDFQE LCLVLGSHMV YLAEKASSLE EARHMLEKAM 300
    KDGSALQTFK TFLAAQGGDA SVVDDPSKLP QAKYIIELEA KEDGYVSEIV 350
    ADAVGTAAMW LGAGRATKES TIDLAVGLVL RKKVGDAVKK GESLVTIYSN 400
    REQVDDVKQK LYENIRISAT PVQAPTLIYD KIS 433
    Length:433
    Mass (Da):46,332
    Last modified:February 1, 1997 - v1
    Checksum:i75EF04B8E7B2E0AD
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D87961 Genomic DNA. Translation: BAA13512.1.
    D87959 Genomic DNA. Translation: BAA20903.1.
    PIRiJT0875.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D87961 Genomic DNA. Translation: BAA13512.1 .
    D87959 Genomic DNA. Translation: BAA20903.1 .
    PIRi JT0875.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1BRW X-ray 2.10 A/B 1-432 [» ]
    ProteinModelPortali P77836.
    SMRi P77836. Positions 1-432.
    ModBasei Search...
    MobiDBi Search...

    Proteomic databases

    PRIDEi P77836.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Enzyme and pathway databases

    BioCyci MetaCyc:MONOMER-17881.

    Miscellaneous databases

    EvolutionaryTracei P77836.

    Family and domain databases

    Gene3Di 3.40.1030.10. 1 hit.
    3.90.1170.30. 1 hit.
    InterProi IPR000312. Glycosyl_Trfase_fam3.
    IPR017459. Glycosyl_Trfase_fam3_N_dom.
    IPR013102. PYNP_C.
    IPR018090. Pyrmidine_PPas_bac/euk.
    IPR000053. Pyrmidine_PPase.
    IPR017872. Pyrmidine_PPase_CS.
    [Graphical view ]
    PANTHERi PTHR10515. PTHR10515. 1 hit.
    Pfami PF02885. Glycos_trans_3N. 1 hit.
    PF00591. Glycos_transf_3. 1 hit.
    PF07831. PYNP_C. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF000478. TP_PyNP. 1 hit.
    SMARTi SM00941. PYNP_C. 1 hit.
    [Graphical view ]
    SUPFAMi SSF47648. SSF47648. 1 hit.
    SSF52418. SSF52418. 1 hit.
    SSF54680. SSF54680. 1 hit.
    TIGRFAMsi TIGR02644. Y_phosphoryl. 1 hit.
    PROSITEi PS00647. THYMID_PHOSPHORYLASE. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Molecular cloning and expression of the pyrimidine nucleoside phosphorylase gene from Bacillus stearothermophilus TH 6-2."
      Okuyama K., Hamamoto T., Noguchi T., Midorikawa Y.
      Biosci. Biotechnol. Biochem. 60:1655-1659(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: TH 6-2.
    2. "The crystal structure of pyrimidine nucleoside phosphorylase in a closed conformation."
      Pugmire M.J., Ealick S.E.
      Structure 6:1467-1479(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).

    Entry informationi

    Entry nameiPDP_GEOSE
    AccessioniPrimary (citable) accession number: P77836
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: February 1, 1997
    Last modified: October 1, 2014
    This is version 97 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3