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NCBI: 03-AUG-2016

Summary[edit | edit source]

  • organism: Staphylococcus aureus NCTC8325
  • locus tag: SAOUHSC_00499
  • pan locus tag?: SAUPAN002283000
  • symbol: SAOUHSC_00499
  • pan gene symbol?: pdxS
  • synonym:
  • product: pyridoxal biosynthesis lyase PdxS

Genome View[edit | edit source]

Gene[edit | edit source]

General[edit | edit source]

  • type: CDS
  • locus tag: SAOUHSC_00499
  • symbol: SAOUHSC_00499
  • product: pyridoxal biosynthesis lyase PdxS
  • replicon: chromosome
  • strand: +
  • coordinates: 500138..501025
  • length: 888
  • essential: no DEG 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
    ATGAGTAAAATTATTGGATCAGACAGAGTCAAAAGAGGTATGGCTGAAATGCAAAAAGGC
    GGCGTTATTATGGATGTCGTTAATGCTGAGCAAGCAAGAATTGCAGAAGAAGCTGGCGCG
    GTAGCAGTTATGGCATTAGAACGAGTACCTTCTGATATTAGAGCTGCTGGTGGTGTTGCA
    CGTATGGCAAACCCTAAAATTGTAGAAGAAGTAATGAATGCTGTTTCTATTCCAGTCATG
    GCTAAAGCACGTATTGGTCATATCACTGAAGCAAGAGTATTAGAGGCGATGGGTGTTGAC
    TATATTGATGAATCAGAAGTGTTAACACCAGCAGATGAGGAATATCACTTAAGAAAAGAT
    CAATTTACAGTACCATTTGTATGTGGATGTCGTAATTTAGGTGAAGCTGCGCGTAGAATT
    GGTGAAGGTGCTGCTATGTTACGTACTAAAGGTGAACCAGGTACAGGTAATATTGTTGAA
    GCTGTAAGACATATGAGACAAGTTAATTCAGAAGTTAGTCGATTGACTGTAATGAATGAT
    GATGAGATTATGACTTTTGCGAAAGATATCGGTGCGCCTTATGAAATTTTAAAACAAATT
    AAAGACAATGGTCGTTTACCGGTAGTTAACTTTGCAGCTGGTGGCGTTGCGACTCCTCAA
    GATGCTGCTTTAATGATGGAATTAGGTGCTGACGGTGTATTCGTTGGATCAGGTATTTTT
    AAATCAGAAGATCCAGAAAAATTTGCTAAAGCAATTGTTCAAGCAACAACACATTACCAA
    GACTATGAACTAATTGGAAGATTAGCAAGTGAACTTGGCACTGCTATGAAAGGTTTAGAT
    ATCAATCAATTATCATTAGAAGAACGTATGCAAGAGCGTGGTTGGTAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    888

Protein[edit | edit source]

General[edit | edit source]

  • locus tag: SAOUHSC_00499
  • symbol: SAOUHSC_00499
  • description: pyridoxal biosynthesis lyase PdxS
  • length: 295
  • theoretical pI: 4.83393
  • theoretical MW: 31992.6
  • GRAVY: -0.130847

Function[edit | edit source]

  • reaction:
    EC 4.3.3.6?  ExPASy
    Pyridoxal 5'-phosphate synthase (glutamine hydrolyzing) D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine = pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate
  • TIGRFAM:
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Pyridoxine pyridoxal 5'-phosphate synthase, synthase subunit Pdx1 (TIGR00343; HMM-score: 505.6)
    and 15 more
    Unknown function General putative TIM-barrel protein, nifR3 family (TIGR00737; HMM-score: 32.5)
    putative enoyl-[acyl-carrier-protein] reductase II (TIGR03151; EC 1.3.1.-; HMM-score: 23.2)
    glycosyl amidation-associated protein WbuZ (TIGR03572; HMM-score: 20.5)
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Thiamine thiamine-phosphate diphosphorylase (TIGR00693; EC 2.5.1.3; HMM-score: 19.7)
    Metabolism Energy metabolism Glycolysis/gluconeogenesis triose-phosphate isomerase (TIGR00419; EC 5.3.1.1; HMM-score: 18.2)
    3-hexulose-6-phosphate synthase (TIGR03128; EC 4.1.2.43; HMM-score: 18)
    Metabolism Amino acid biosynthesis Histidine family 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase (TIGR00007; EC 5.3.1.16; HMM-score: 17.1)
    Metabolism Amino acid biosynthesis Aromatic amino acid family tryptophan synthase, alpha subunit (TIGR00262; EC 4.2.1.20; HMM-score: 16.7)
    Metabolism Purines, pyrimidines, nucleosides, and nucleotides Pyrimidine ribonucleotide biosynthesis orotidine 5'-phosphate decarboxylase (TIGR01740; EC 4.1.1.23; HMM-score: 16.4)
    dihydroorotate dehydrogenase family protein (TIGR01037; EC 1.3.-.-; HMM-score: 15.8)
    Unknown function General hisA/hisF family protein (TIGR00734; HMM-score: 15.6)
    methylmalonyl-CoA mutase C-terminal domain (TIGR00640; HMM-score: 15.1)
    Metabolism Amino acid biosynthesis Histidine family imidazoleglycerol phosphate synthase, cyclase subunit (TIGR00735; HMM-score: 15.1)
    geranylgeranylglyceryl phosphate synthase family protein (TIGR01768; EC 2.5.1.-; HMM-score: 13.4)
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Other isopentenyl-diphosphate delta-isomerase, type 2 (TIGR02151; EC 5.3.3.2; HMM-score: 12.7)
  • TheSEED:  
    Cofactors, Vitamins, Prosthetic Groups, Pigments Pyridoxine Pyridoxin (Vitamin B6) Biosynthesis  Pyridoxine biosynthesis glutamine amidotransferase, synthase subunit (EC 2.4.2.-)
    and 1 more
    Test Pyridoxin B6  Pyridoxine biosynthesis glutamine amidotransferase, synthase subunit (EC 2.4.2.-)
  • PFAM:
    TIM_barrel (CL0036) SOR_SNZ; SOR/SNZ family (PF01680; HMM-score: 356.8)
    and 12 more
    ThiG; Thiazole biosynthesis protein ThiG (PF05690; HMM-score: 46.9)
    Dus; Dihydrouridine synthase (Dus) (PF01207; HMM-score: 28.8)
    IGPS; Indole-3-glycerol phosphate synthase (PF00218; HMM-score: 24.4)
    His_biosynth; Histidine biosynthesis protein (PF00977; HMM-score: 22.8)
    NMO; Nitronate monooxygenase (PF03060; HMM-score: 22.3)
    NanE; Putative N-acetylmannosamine-6-phosphate epimerase (PF04131; HMM-score: 21.1)
    OMPdecase; Orotidine 5'-phosphate decarboxylase / HUMPS family (PF00215; HMM-score: 20.4)
    DUF561; Protein of unknown function (DUF561) (PF04481; HMM-score: 17.3)
    IMPDH; IMP dehydrogenase / GMP reductase domain (PF00478; HMM-score: 15.5)
    FMN_dh; FMN-dependent dehydrogenase (PF01070; HMM-score: 15.5)
    TMP-TENI; Thiamine monophosphate synthase (PF02581; HMM-score: 15)
    no clan defined Phage_Cox; Regulatory phage protein cox (PF10743; HMM-score: 13.5)

Structure, modifications & interactions[edit | edit source]

Localization[edit | edit source]

  • PSORTb: Cytoplasmic
    • Cytoplasmic Score: 7.5
    • Cytoplasmic Membrane Score: 1.15
    • Cellwall Score: 0.62
    • Extracellular Score: 0.73
    • 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): 0.004504
    • TAT(Tat/SPI): 0.001201
    • LIPO(Sec/SPII): 0.000466
  • predicted transmembrane helices (TMHMM): 0

Accession numbers[edit | edit source]

Protein sequence[edit | edit source]

  • MSKIIGSDRVKRGMAEMQKGGVIMDVVNAEQARIAEEAGAVAVMALERVPSDIRAAGGVARMANPKIVEEVMNAVSIPVMAKARIGHITEARVLEAMGVDYIDESEVLTPADEEYHLRKDQFTVPFVCGCRNLGEAARRIGEGAAMLRTKGEPGTGNIVEAVRHMRQVNSEVSRLTVMNDDEIMTFAKDIGAPYEILKQIKDNGRLPVVNFAAGGVATPQDAALMMELGADGVFVGSGIFKSEDPEKFAKAIVQATTHYQDYELIGRLASELGTAMKGLDINQLSLEERMQERGW

Experimental data[edit | edit source]

Expression & Regulation[edit | edit source]

Operon[edit | edit source]

Regulation[edit | edit source]

  • regulator: PdxR* (activation) regulon
    PdxR(TF)important in Pyridoxine biosynthesis; compare RegPrecise for N315   [4]

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. 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 1.14 1.15 1.16 1.17 1.18 1.19 1.20 1.21 1.22 1.23 1.24 1.25 1.26 1.27 1.28 1.29 1.30 1.31 1.32 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. 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)
  3. 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)
  4. 4.0 4.1 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 | edit source]