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NCBI: 03-AUG-2016

Summary[edit source | edit]

  • organism: Staphylococcus aureus NCTC8325
  • locus tag: SAOUHSC_02377
  • pan locus tag?: SAUPAN005432000
  • symbol: SAOUHSC_02377
  • 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: SAOUHSC_02377
  • symbol: SAOUHSC_02377
  • product: pyrimidine-nucleoside phosphorylase
  • replicon: chromosome
  • strand: -
  • coordinates: 2199608..2200909
  • 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
    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 source | edit]

Protein Data Bank: 3H5Q

General[edit source | edit]

  • locus tag: SAOUHSC_02377
  • symbol: SAOUHSC_02377
  • description: pyrimidine-nucleoside phosphorylase
  • length: 433
  • theoretical pI: 4.71387
  • theoretical MW: 46307.8
  • GRAVY: -0.0226328

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: 599.8)
    MetabolismPurines, pyrimidines, nucleosides, and nucleotidesOtherthymidine 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)
    MetabolismAmino acid biosynthesisAromatic amino acid familyanthranilate phosphoribosyltransferase (TIGR01245; EC 2.4.2.18; HMM-score: 33.8)
  • 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: 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 source | edit]

  • domains:
  • modifications:
  • cofactors: K+
  • effectors:
  • protein partners:
    SAOUHSC_02509(rplB)50S ribosomal protein L2  [1] (data from MRSA252)
    SAOUHSC_01784(rplT)50S ribosomal protein L20  [1] (data from MRSA252)
    SAOUHSC_02494(rpsE)30S ribosomal protein S5  [1] (data from MRSA252)
    SAOUHSC_01040pyruvate dehydrogenase complex, E1 component subunit alpha  [1] (data from MRSA252)
    SAOUHSC_01197glycerol-3-phosphate acyltransferase PlsX  [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: 0.116
    • Ymax_pos: 11
    • Cmax: 0.135
    • Cmax_pos: 32
    • Smax: 0.209
    • Smax_pos: 2
    • Smean: 0.123
    • D: 0.119
  • predicted transmembrane helices (TMHMM): 0

Accession numbers[edit source | edit]

Protein sequence[edit source | edit]

  • MRMIDIIEKKRDGHTLTTEEINFFIGGYVKGDIPDYQASSLAMAIYFQDMNDDERAALTMAMVNSGDMIDLSDIKGVKVDKHSTGGVGDTTTLVLAPLVAAVDVPVAKMSGRGLGHTGGTIDKLEAIDGFHVEIDEATFVKLVNENKVAVVGQSGNLTPADKKLYALRDVTGTVNSIPLIASSIMSKKIAAGADAIVLDVKTGSGAFMKTLEDAEALAHAMVRIGNNVGRNTMAIISDMNQPLGRAIGNALELQEAIDTLKGQGPKDLTELVLTLGSQMVVLANKAETLEEARALLIEAINSGAALEKFKTFIKNQGGDETVIDHPERLPQAQYQIEYKAKKSGYVTELVSNDIGVASMMLGAGRLTKEDDIDLAVGIVLNKKIGDKVEEGESLLTIHSNRQDVDDVVKKLDSSITIADHVVSPTLIHKIITE

Experimental data[edit source | edit]

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)
  2. Stephan Michalik, Maren Depke, Annette Murr, Manuela Gesell Salazar, Ulrike Kusebauch, Zhi Sun, Tanja C Meyer, Kristin Surmann, Henrike Pförtner, Petra Hildebrandt, Stefan Weiss, Laura Marcela Palma Medina, Melanie Gutjahr, Elke Hammer, Dörte Becher, Thomas Pribyl, Sven Hammerschmidt, Eric W Deutsch, Samuel L Bader, Michael Hecker, Robert L Moritz, Ulrike Mäder, Uwe Völker, Frank Schmidt
    A global Staphylococcus aureus proteome resource applied to the in vivo characterization of host-pathogen interactions.
    Sci Rep: 2017, 7(1);9718
    [PubMed:28887440] [WorldCat.org] [DOI] (I e)
  3. Maren Depke, Stephan Michalik, Alexander Rabe, Kristin Surmann, Lars Brinkmann, Nico Jehmlich, Jörg Bernhardt, Michael Hecker, Bernd Wollscheid, Zhi Sun, Robert L Moritz, Uwe Völker, Frank Schmidt
    A peptide resource for the analysis of Staphylococcus aureus in host-pathogen interaction studies.
    Proteomics: 2015, 15(21);3648-61
    [PubMed:26224020] [WorldCat.org] [DOI] (I p)
  4. Ulrike Mäder, Pierre Nicolas, Maren Depke, Jan Pané-Farré, Michel Debarbouille, Magdalena M van der Kooi-Pol, Cyprien Guérin, Sandra Dérozier, Aurelia Hiron, Hanne Jarmer, Aurélie Leduc, Stephan Michalik, Ewoud Reilman, Marc Schaffer, Frank Schmidt, Philippe Bessières, Philippe Noirot, Michael Hecker, Tarek Msadek, Uwe Völker, Jan Maarten van Dijl
    Staphylococcus aureus Transcriptome Architecture: From Laboratory to Infection-Mimicking Conditions.
    PLoS Genet.: 2016, 12(4);e1005962
    [PubMed:27035918] [WorldCat.org] [DOI] (I e)

Relevant publications[edit source | edit]