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NCBI: 26-AUG-2013

Summary[edit source | edit]

  • organism: Staphylococcus aureus N315
  • locus tag: SA1938 [new locus tag: SA_RS11130 ]
  • pan locus tag?: SAUPAN005432000
  • symbol: pdp
  • pan gene symbol?: pdp
  • synonym:
  • product: pyrimidine-nucleoside phosphorylase

Genome View[edit source | edit]

Gene[edit source | edit]

General[edit source | edit]

  • type: CDS
  • locus tag: SA1938 [new locus tag: SA_RS11130 ]
  • symbol: pdp
  • product: pyrimidine-nucleoside phosphorylase
  • replicon: chromosome
  • strand: -
  • coordinates: 2187346..2188647
  • length: 1302
  • essential: no DEG other strains

Accession numbers[edit source | edit]

Phenotype[edit source | edit]

  • Share your knowledge and add information here. [edit]

DNA sequence[edit source | edit]

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

Protein[edit source | edit]

General[edit source | edit]

  • locus tag: SA1938 [new locus tag: SA_RS11130 ]
  • symbol: Pdp
  • description: pyrimidine-nucleoside phosphorylase
  • length: 433
  • theoretical pI: 4.67207
  • theoretical MW: 46365.8
  • GRAVY: -0.0297921

Function[edit source | edit]

  • reaction:
    EC 2.4.2.2?  ExPASy
    Pyrimidine-nucleoside phosphorylaseUridine + phosphate = uracil + alpha-D-ribose 1-phosphateThymidine + phosphate = thymine + 2-deoxy-alpha-D-ribose 1-phosphate2'-deoxyuridine + phosphate = uracil + 2-deoxy-alpha-D-ribose 1-phosphate
  • TIGRFAM:
    MetabolismPurines, pyrimidines, nucleosides, and nucleotidesOtherpyrimidine-nucleoside phosphorylase (TIGR02644; EC 2.4.2.2; HMM-score: 600.9)
    MetabolismPurines, pyrimidines, nucleosides, and nucleotidesOtherthymidine phosphorylase (TIGR02643; EC 2.4.2.4; HMM-score: 452.6)
    putative thymidine phosphorylase (TIGR02645; EC 2.4.2.4; HMM-score: 239.7)
    AMP phosphorylase (TIGR03327; EC 2.4.-.-; HMM-score: 236.7)
    MetabolismAmino acid biosynthesisAromatic amino acid familyanthranilate phosphoribosyltransferase (TIGR01245; EC 2.4.2.18; HMM-score: 35.4)
  • TheSEED:  
    CarbohydratesMonosaccharidesDeoxyribose and Deoxynucleoside Catabolism Pyrimidine-nucleoside phosphorylase (EC 2.4.2.2) 
    Nucleosides and NucleotidesPyrimidinespyrimidine conversions Pyrimidine-nucleoside phosphorylase (EC 2.4.2.2) 
  • PFAM:
    no clan definedGlycos_transf_3; Glycosyl transferase family, a/b domain (PF00591; HMM-score: 165.3)
    Hybrid (CL0105) PYNP_C; Pyrimidine nucleoside phosphorylase C-terminal domain (PF07831; HMM-score: 93.9)
    no clan definedGlycos_trans_3N; Glycosyl transferase family, helical bundle domain (PF02885; HMM-score: 82.3)
    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 source | edit]

  • domains:
  • modifications:
  • cofactors: K+
  • effectors:
  • protein partners:
    SA0943-1(pdhA)pyruvate dehydrogenase E1 component subunit alpha  [1] (data from MRSA252)
    SA1072(plsX)glycerol-3-phosphate acyltransferase PlsX  [1] (data from MRSA252)
    SA2044(rplB)50S ribosomal protein L2  [1] (data from MRSA252)
    SA1502(rplT)50S ribosomal protein L20  [1] (data from MRSA252)
    SA2031(rpsE)30S ribosomal protein S5  [1] (data from MRSA252)

Localization[edit source | edit]

  • 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
    • Ymax: 0.114
    • Ymax_pos: 11
    • Cmax: 0.135
    • Cmax_pos: 32
    • Smax: 0.209
    • Smax_pos: 2
    • Smean: 0.118
    • D: 0.115
  • predicted transmembrane helices (TMHMM): 0

Accession numbers[edit source | edit]

Protein sequence[edit source | edit]

  • MRMIDIIEKKRDGHTLTTEEINFFIDGYVKGDIPDYQASSLAMAIYFQDMNDDERAALTMAMVNSGDMIDLSDIKGVKVDKHSTGGVGDTTTLVLAPLVAAVDVPVAKMSGRGLGHTGGTIDKLEAIDGFHVEIDEATFVKLVNENKVAVVGQSGNLTPADKKLYALRDVTGTVNSIPLIASSIMSKKIAAGADAIVLDVKTGSGAFMKTLEDAEALAHAMVRIGNNVGRNTMAIISDMNQPLGRAIGNALELQEAIDTLKGQGPKDLTELVLTLGSQMVVLANKAETLEEARALLIEAINSGAALEKFKTFIKNQGGDETVIDHPERLPQAQYQIEYKAKKSGYVTELVSNDIGVASMMLGAGRLTKEDDIDLAVGIVLNKKIGDKVEEGESLLTIHSNRQDVDDVVKKLDSSITIADHVVSPTLIHKIITE

Experimental data[edit source | edit]

  • experimentally validated: no data available

Expression & Regulation[edit source | edit]

Operon[edit source | edit]

Regulation[edit source | edit]

  • sigma factor:
  • regulator:

Transcription pattern[edit source | edit]

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

Protein stability[edit source | edit]

  • half-life: no data available

Biological Material[edit source | edit]

Mutants[edit source | edit]

Expression vector[edit source | edit]

lacZ fusion[edit source | edit]

GFP fusion[edit source | edit]

two-hybrid system[edit source | edit]

FLAG-tag construct[edit source | edit]

Antibody[edit source | edit]

Other Information[edit source | edit]

You are kindly invited to share additional interesting facts.

Literature[edit source | edit]

References[edit source | edit]

  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 source | edit]

Alexander Scherl, Patrice François, Manuela Bento, Jacques M Deshusses, Yvan Charbonnier, Véronique Converset, Antoine Huyghe, Nadia Walter, Christine Hoogland, Ron D Appel, Jean-Charles Sanchez, Catherine G Zimmermann-Ivol, Garry L Corthals, Denis F Hochstrasser, Jacques Schrenzel
Correlation of proteomic and transcriptomic profiles of Staphylococcus aureus during the post-exponential phase of growth.
J. Microbiol. Methods: 2005, 60(2);247-57
[PubMed:15590099] [WorldCat.org] [DOI] (P p)