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NCBI: 10-JUN-2013

Summary[edit | edit source]

  • organism: Staphylococcus aureus COL
  • locus tag: SACOL2128 [new locus tag: SACOL_RS11135 ]
  • pan locus tag?: SAUPAN005432000
  • symbol: pdp
  • pan gene symbol?: pdp
  • synonym:
  • product: pyrimidine-nucleoside phosphorylase

Genome View[edit | edit source]

Gene[edit | edit source]

General[edit | edit source]

  • type: CDS
  • locus tag: SACOL2128 [new locus tag: SACOL_RS11135 ]
  • symbol: pdp
  • product: pyrimidine-nucleoside phosphorylase
  • replicon: chromosome
  • strand: -
  • coordinates: 2188884..2190185
  • 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: SACOL2128 [new locus tag: SACOL_RS11135 ]
  • 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:  
    Carbohydrates Monosaccharides Deoxyribose and Deoxynucleoside Catabolism  Pyrimidine-nucleoside phosphorylase (EC 2.4.2.2)
    and 1 more
    Nucleosides and Nucleotides Pyrimidines pyrimidine conversions  Pyrimidine-nucleoside phosphorylase (EC 2.4.2.2)
  • 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 & interactions[edit | edit source]

  • domains:
  • modifications:
  • cofactors: K+
  • effectors:
  • protein partners:
    SACOL1102(pdhA)pyruvate dehydrogenase complex E1 component subunit alpha  [1] (data from MRSA252)
    SACOL1243(plsX)glycerol-3-phosphate acyltransferase PlsX  [1] (data from MRSA252)
    SACOL2236(rplB)50S ribosomal protein L2  [1] (data from MRSA252)
    SACOL1725(rplT)50S ribosomal protein L20  [1] (data from MRSA252)
    SACOL2222(rpsE)30S ribosomal protein S5  [1] (data from MRSA252)

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: PeptideAtlas
    experimental localization: Cytoplasmic [2] [3] [4]
    quantitative data / protein copy number per cell: 40 [5]

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)
  2. Dörte Becher, Kristina Hempel, Susanne Sievers, Daniela Zühlke, Jan Pané-Farré, Andreas Otto, Stephan Fuchs, Dirk Albrecht, Jörg Bernhardt, Susanne Engelmann, Uwe Völker, Jan Maarten van Dijl, Michael Hecker
    A proteomic view of an important human pathogen--towards the quantification of the entire Staphylococcus aureus proteome.
    PLoS One: 2009, 4(12);e8176
    [PubMed:19997597] [WorldCat.org] [DOI] (I e)
  3. Kristina Hempel, Florian-Alexander Herbst, Martin Moche, Michael Hecker, Dörte Becher
    Quantitative proteomic view on secreted, cell surface-associated, and cytoplasmic proteins of the methicillin-resistant human pathogen Staphylococcus aureus under iron-limited conditions.
    J Proteome Res: 2011, 10(4);1657-66
    [PubMed:21323324] [WorldCat.org] [DOI] (I p)
  4. Andreas Otto, Jan Maarten van Dijl, Michael Hecker, Dörte Becher
    The Staphylococcus aureus proteome.
    Int J Med Microbiol: 2014, 304(2);110-20
    [PubMed:24439828] [WorldCat.org] [DOI] (I p)
  5. Daniela Zühlke, Kirsten Dörries, Jörg Bernhardt, Sandra Maaß, Jan Muntel, Volkmar Liebscher, Jan Pané-Farré, Katharina Riedel, Michael Lalk, Uwe Völker, Susanne Engelmann, Dörte Becher, Stephan Fuchs, Michael Hecker
    Costs of life - Dynamics of the protein inventory of Staphylococcus aureus during anaerobiosis.
    Sci Rep: 2016, 6;28172
    [PubMed:27344979] [WorldCat.org] [DOI] (I e)

Relevant publications[edit | edit source]