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NCBI: 06-JUL-2013

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus Newman
  • locus tag: NWMN_2040 [new locus tag: NWMN_RS11780 ]
  • pan locus tag?: SAUPAN005432000
  • symbol: pdp
  • pan gene symbol?: pdp
  • synonym: deoA
  • product: pyrimidine-nucleoside phosphorylase

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: NWMN_2040 [new locus tag: NWMN_RS11780 ]
  • symbol: pdp
  • product: pyrimidine-nucleoside phosphorylase
  • replicon: chromosome
  • strand: -
  • coordinates: 2257267..2258568
  • length: 1302
  • essential: unknown other strains

⊟Accession numbers[edit | edit source]

⊟Phenotype[edit | edit source]

Share your knowledge and add information here. [edit]

⊟DNA sequence[edit | edit source]

  • 1
    61
    121
    181
    241
    301
    361
    421
    481
    541
    601
    661
    721
    781
    841
    901
    961
    1021
    1081
    1141
    1201
    1261
    ATGAGAATGATAGACATTATTGAGAAAAAGCGTGACGGTCATACACTAACAACGGAAGAA
    ATTAATTTCTTTATTGGCGGCTATGTTAAAGGGGATATTCCTGATTACCAAGCATCAAGT
    TTAGCAATGGCGATTTATTTCCAAGATATGAATGATGATGAGCGTGCAGCATTAACGATG
    GCTATGGTTAATTCTGGTGATATGATAGATTTGAGTGATATTAAAGGTGTCAAAGTAGAT
    AAGCACTCAACAGGTGGTGTAGGAGATACAACTACATTGGTTTTAGCACCATTAGTAGCA
    GCTGTAGATGTTCCTGTTGCAAAAATGAGTGGGCGTGGATTAGGTCATACAGGTGGTACG
    ATTGATAAATTAGAAGCAATTGATGGTTTTCATGTTGAAATAGATGAAGCAACATTTGTG
    AAATTGGTTAATGAAAATAAAGTGGCAGTTGTAGGACAATCAGGAAATTTAACTCCTGCA
    GACAAAAAATTATATGCCTTAAGGGATGTTACTGGTACTGTCAATTCAATACCATTAATT
    GCCTCTTCAATTATGAGTAAAAAGATTGCTGCTGGTGCAGATGCAATTGTATTAGATGTA
    AAAACTGGTAGCGGTGCATTTATGAAAACATTAGAAGATGCTGAAGCATTAGCGCACGCA
    ATGGTACGTATTGGTAATAATGTGGGACGTAATACGATGGCGATTATTTCTGATATGAAT
    CAGCCACTTGGACGTGCGATTGGCAATGCGCTTGAGTTACAAGAAGCAATTGATACGTTG
    AAAGGACAAGGTCCGAAAGATTTAACAGAACTTGTATTAACATTAGGTTCTCAAATGGTT
    GTACTTGCAAACAAAGCTGAAACGCTTGAAGAAGCGAGAGCGTTGCTAATTGAGGCAATT
    AATTCAGGTGCAGCATTAGAAAAATTCAAAACATTTATTAAAAACCAAGGTGGCGACGAA
    ACTGTTATTGACCATCCAGAGCGTTTGCCACAAGCTCAATATCAAATTGAATATAAAGCT
    AAAAAATCAGGTTATGTGACTGAATTAGTCTCTAACGATATAGGTGTCGCTTCGATGATG
    TTAGGAGCGGGACGTTTAACAAAAGAGGATGATATTGATTTAGCGGTTGGTATTGTTTTA
    AATAAAAAAATTGGTGATAAAGTAGAAGAAGGAGAATCATTATTAACGATTCACAGTAAT
    CGCCAAGATGTAGACGATGTTGTTAAAAAATTAGATTCAAGCATAACAATTGCTGATCAT
    GTTGTATCGCCTACATTAATTCATAAAATCATTACAGAATAG
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    900
    960
    1020
    1080
    1140
    1200
    1260
    1302

⊟Protein[edit | edit source]

Protein Data Bank: 3H5Q

⊟General[edit | edit source]

  • locus tag: NWMN_2040 [new locus tag: NWMN_RS11780 ]
  • symbol: Pdp
  • description: pyrimidine-nucleoside phosphorylase
  • length: 433
  • theoretical pI: 4.71387
  • theoretical MW: 46307.8
  • GRAVY: -0.0226328

⊟Function[edit | edit source]

  • reaction:
    EC 2.4.2.2?  ExPASy
    Pyrimidine-nucleoside phosphorylase 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
  • TIGRFAM:
    Metabolism Purines, pyrimidines, nucleosides, and nucleotides Other pyrimidine-nucleoside phosphorylase (TIGR02644; EC 2.4.2.2; HMM-score: 599.8)
    and 4 more
    Metabolism Purines, pyrimidines, nucleosides, and nucleotides Other thymidine phosphorylase (TIGR02643; EC 2.4.2.4; HMM-score: 451.7)
    putative thymidine phosphorylase (TIGR02645; EC 2.4.2.4; HMM-score: 238.7)
    AMP phosphorylase (TIGR03327; EC 2.4.-.-; HMM-score: 234.9)
    Metabolism Amino acid biosynthesis Aromatic amino acid family anthranilate phosphoribosyltransferase (TIGR01245; EC 2.4.2.18; HMM-score: 33.8)
  • TheSEED: data available for COL, N315, NCTC8325, USA300_FPR3757
  • PFAM:
    no clan defined Glycos_transf_3; Glycosyl transferase family, a/b domain (PF00591; HMM-score: 165.3)
    and 4 more
    Hybrid (CL0105) PYNP_C; Pyrimidine nucleoside phosphorylase C-terminal domain (PF07831; HMM-score: 93.9)
    no clan defined Glycos_trans_3N; Glycosyl transferase family, helical bundle domain (PF02885; HMM-score: 80.7)
    Hybrid (CL0105) HlyD_D23; Barrel-sandwich domain of CusB or HlyD membrane-fusion (PF16576; HMM-score: 12.8)
    Glycine-zipper (CL0500) DUF1269; Protein of unknown function (DUF1269) (PF06897; HMM-score: 10.9)

⊟Structure, modifications & cofactors[edit | edit source]

  • domains:
  • modifications:
  • cofactors:
  • effectors:

⊟Localization[edit | edit source]

  • PSORTb: unknown (no significant prediction)
    • Cytoplasmic Score: 2.5
    • Cytoplasmic Membrane Score: 2.5
    • Cellwall Score: 2.5
    • Extracellular Score: 2.5
    • Internal Helices: 0
  • LocateP: Intracellular
    • Prediction by SwissProt Classification: Cytoplasmic
    • Pathway Prediction: No pathway
    • Intracellular possibility: 1
    • Signal peptide possibility: -1
    • N-terminally Anchored Score: 1
    • Predicted Cleavage Site: No CleavageSite
  • SignalP: no predicted signal peptide
    • SP(Sec/SPI): 0.004747
    • TAT(Tat/SPI): 0.000301
    • LIPO(Sec/SPII): 0.000545
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MRMIDIIEKKRDGHTLTTEEINFFIGGYVKGDIPDYQASSLAMAIYFQDMNDDERAALTMAMVNSGDMIDLSDIKGVKVDKHSTGGVGDTTTLVLAPLVAAVDVPVAKMSGRGLGHTGGTIDKLEAIDGFHVEIDEATFVKLVNENKVAVVGQSGNLTPADKKLYALRDVTGTVNSIPLIASSIMSKKIAAGADAIVLDVKTGSGAFMKTLEDAEALAHAMVRIGNNVGRNTMAIISDMNQPLGRAIGNALELQEAIDTLKGQGPKDLTELVLTLGSQMVVLANKAETLEEARALLIEAINSGAALEKFKTFIKNQGGDETVIDHPERLPQAQYQIEYKAKKSGYVTELVSNDIGVASMMLGAGRLTKEDDIDLAVGIVLNKKIGDKVEEGESLLTIHSNRQDVDDVVKKLDSSITIADHVVSPTLIHKIITE

⊟Experimental data[edit | edit source]

  • experimentally validated: data available for COL, NCTC8325
  • protein localization: data available for COL
  • quantitative data / protein copy number per cell: data available for COL
  • interaction partners:
    NWMN_0959(phdA)pyruvate dehydrogenase E1 component, alpha subunit  [1] (data from MRSA252)
    NWMN_1139(plsX)putative glycerol-3-phosphate acyltransferase PlsX  [1] (data from MRSA252)
    NWMN_2149(rplB)50S ribosomal protein L2  [1] (data from MRSA252)
    NWMN_1572(rplT)50S ribosomal protein L20  [1] (data from MRSA252)
    NWMN_2135(rpsE)30S ribosomal protein S5  [1] (data from MRSA252)

⊟Expression & Regulation[edit | edit source]

⊟Operon[edit | edit source]

⊟Regulation[edit | edit source]

  • regulator:

⊟Transcription pattern[edit | edit source]

⊟Protein synthesis (provided by Aureolib)[edit | edit source]

⊟Protein stability[edit | edit source]

  • half-life: no data available

⊟Biological Material[edit | edit source]

⊟Mutants[edit | edit source]

⊟Expression vector[edit | edit source]

⊟lacZ fusion[edit | edit source]

⊟GFP fusion[edit | edit source]

⊟two-hybrid system[edit | edit source]

⊟FLAG-tag construct[edit | edit source]

⊟Antibody[edit | edit source]

⊟Other Information[edit | edit source]

You are kindly invited to share additional interesting facts.

⊟Literature[edit | edit source]

⊟References[edit | edit source]

  1. ↑ 1.0 1.1 1.2 1.3 1.4 Artem Cherkasov, Michael Hsing, Roya Zoraghi, Leonard J Foster, Raymond H See, Nikolay Stoynov, Jihong Jiang, Sukhbir Kaur, Tian Lian, Linda Jackson, Huansheng Gong, Rick Swayze, Emily Amandoron, Farhad Hormozdiari, Phuong Dao, Cenk Sahinalp, Osvaldo Santos-Filho, Peter Axerio-Cilies, Kendall Byler, William R McMaster, Robert C Brunham, B Brett Finlay, Neil E Reiner
    Mapping the protein interaction network in methicillin-resistant Staphylococcus aureus.
    J Proteome Res: 2011, 10(3);1139-50
    [PubMed:21166474] [WorldCat.org] [DOI] (I p)

⊟Relevant publications[edit | edit source]

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