From AureoWiki
Jump to navigation Jump to search

NCBI: 10-JUN-2013

Summary[edit | edit source]

  • organism: Staphylococcus aureus COL
  • locus tag: SACOL1666 [new locus tag: SACOL_RS08500 ]
  • pan locus tag?: SAUPAN004207000
  • symbol: udk
  • pan gene symbol?: udk
  • synonym:
  • product: uridine kinase

Genome View[edit | edit source]

Gene[edit | edit source]

General[edit | edit source]

  • type: CDS
  • locus tag: SACOL1666 [new locus tag: SACOL_RS08500 ]
  • symbol: udk
  • product: uridine kinase
  • replicon: chromosome
  • strand: -
  • coordinates: 1694389..1695012
  • length: 624
  • 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
    ATGAAAGCTACTACAATCATTGGCATAGCTGGTGGATCTGGCTCAGGAAAAACAACTGTA
    ACTAACGAAATTATGAAAAACTTAGAAGGTCATAGTGTCGCTTTACTTGCTCAAGATTAC
    TATTATAAAGATCAAAAGCACTTGACTTTCGACGAGCGCCTAGAAACCAATTATGACCAT
    CCATTTGCATTCGATAATGATTTATTAATTGAAAATCTTAAAGACTTGAAAAATGGTAAA
    GCAGTAGAAGTACCGACATATGATTATGCTAGTCATACAAGAAGTGACATTACCATTGAT
    TTTAAACCTAAAGATGTTATTATCGTAGAAGGCATTTTCGCTTTAGAAAATAAGGTATTA
    CGTGATATGATGGATGTTAAAATATATGTTGATACAGATGCAGACTTGAGAATATTACGC
    CGTTTAACACGAGATACTAAAGAGCGTGGGCGTTCAATGGACTCTGTTATCAATCAATAT
    TTAAGTGTTGTTAGACCTATGCATGACCAATTTATTGAACCGACTAAGAAATATGCTGAT
    ATAATTATTCCTGAAGGTGGGAGCAATAAAGTTGCAATAGATATTATGACAACAAAAATT
    CAGTCTTTAGTTAGCAAGCAATAG
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    624

Protein[edit | edit source]

General[edit | edit source]

  • locus tag: SACOL1666 [new locus tag: SACOL_RS08500 ]
  • symbol: Udk
  • description: uridine kinase
  • length: 207
  • theoretical pI: 6.03587
  • theoretical MW: 23504.7
  • GRAVY: -0.395652

Function[edit | edit source]

  • reaction:
    EC 2.7.1.48?  ExPASy
    Uridine kinase ATP + uridine = ADP + UMP ATP + cytidine = ADP + CMP?
  • TIGRFAM:
    Metabolism Purines, pyrimidines, nucleosides, and nucleotides Salvage of nucleosides and nucleotides uridine kinase (TIGR00235; EC 2.7.1.48; HMM-score: 294.6)
    and 23 more
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Pantothenate and coenzyme A pantothenate kinase (TIGR00554; EC 2.7.1.33; HMM-score: 36.2)
    putative cytidylate kinase (TIGR02173; EC 2.7.4.14; HMM-score: 26.1)
    Metabolism Purines, pyrimidines, nucleosides, and nucleotides Nucleotide and nucleoside interconversions cytidylate kinase (TIGR00017; EC 2.7.4.14; HMM-score: 20.6)
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Molybdopterin molybdopterin-guanine dinucleotide biosynthesis protein B (TIGR00176; HMM-score: 19.9)
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Pantothenate and coenzyme A dephospho-CoA kinase (TIGR00152; EC 2.7.1.24; HMM-score: 18.9)
    Cellular processes Cellular processes Toxin production and resistance putative bacteriocin export ABC transporter, lactococcin 972 group (TIGR03608; HMM-score: 18.5)
    Metabolism Transport and binding proteins Unknown substrate putative bacteriocin export ABC transporter, lactococcin 972 group (TIGR03608; HMM-score: 18.5)
    Metabolism Central intermediary metabolism Nitrogen metabolism urease accessory protein UreG (TIGR00101; HMM-score: 17.3)
    Metabolism Purines, pyrimidines, nucleosides, and nucleotides Nucleotide and nucleoside interconversions dTMP kinase (TIGR00041; EC 2.7.4.9; HMM-score: 16.3)
    Metabolism Central intermediary metabolism Sulfur metabolism adenylyl-sulfate kinase (TIGR00455; EC 2.7.1.25; HMM-score: 15.5)
    Metabolism Transport and binding proteins Cations and iron carrying compounds nickel import ATP-binding protein NikD (TIGR02770; HMM-score: 14.6)
    P-type DNA transfer ATPase VirB11 (TIGR02788; HMM-score: 14.5)
    Cell structure Cell envelope Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides cellulose synthase operon protein YhjQ (TIGR03371; HMM-score: 13.7)
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Heme, porphyrin, and cobalamin cobalamin biosynthesis protein CobW (TIGR02475; HMM-score: 13.2)
    Genetic information processing DNA metabolism DNA replication, recombination, and repair orc1/cdc6 family replication initiation protein (TIGR02928; HMM-score: 12.9)
    Metabolism Transport and binding proteins Amino acids, peptides and amines LAO/AO transport system ATPase (TIGR00750; EC 2.7.-.-; HMM-score: 12.5)
    Signal transduction Regulatory functions Protein interactions LAO/AO transport system ATPase (TIGR00750; EC 2.7.-.-; HMM-score: 12.5)
    Cellular processes Cellular processes Conjugation P-type conjugative transfer ATPase TrbB (TIGR02782; HMM-score: 12.3)
    Metabolism Central intermediary metabolism Phosphorus compounds phosphonate C-P lyase system protein PhnK (TIGR02323; HMM-score: 11.1)
    Genetic information processing Protein fate Protein and peptide secretion and trafficking type I secretion system ATPase (TIGR01846; HMM-score: 10.8)
    thiol reductant ABC exporter, CydD subunit (TIGR02857; HMM-score: 10.5)
    thiol reductant ABC exporter, CydC subunit (TIGR02868; HMM-score: 10)
    Metabolism Transport and binding proteins Other pigment precursor permease (TIGR00955; HMM-score: 8.7)
  • TheSEED:  
    Nucleosides and Nucleotides Pyrimidines pyrimidine conversions  Uridine kinase (EC 2.7.1.48)
    and 1 more
    Uridine kinase (EC 2.7.1.48) [C1]
  • PFAM:
    P-loop_NTPase (CL0023) PRK; Phosphoribulokinase / Uridine kinase family (PF00485; HMM-score: 157.6)
    and 25 more
    AAA_18; AAA domain (PF13238; HMM-score: 39.7)
    dNK; Deoxynucleoside kinase (PF01712; HMM-score: 23)
    AAA_17; AAA domain (PF13207; HMM-score: 22.5)
    cobW; CobW/HypB/UreG, nucleotide-binding domain (PF02492; HMM-score: 21.2)
    Cytidylate_kin; Cytidylate kinase (PF02224; HMM-score: 20.7)
    CoaE; Dephospho-CoA kinase (PF01121; HMM-score: 20.6)
    ABC_tran; ABC transporter (PF00005; HMM-score: 19.5)
    AAA_33; AAA domain (PF13671; HMM-score: 18.9)
    MobB; Molybdopterin guanine dinucleotide synthesis protein B (PF03205; HMM-score: 17.7)
    RNA_helicase; RNA helicase (PF00910; HMM-score: 17.4)
    AAA_16; AAA ATPase domain (PF13191; HMM-score: 17.1)
    AAA_26; AAA domain (PF13500; HMM-score: 16.9)
    AAA_28; AAA domain (PF13521; HMM-score: 16.2)
    Zeta_toxin; Zeta toxin (PF06414; HMM-score: 16)
    AAA_19; AAA domain (PF13245; HMM-score: 16)
    NTPase_1; NTPase (PF03266; HMM-score: 15.1)
    CbiA; CobQ/CobB/MinD/ParA nucleotide binding domain (PF01656; HMM-score: 14.5)
    ArgK; ArgK protein (PF03308; HMM-score: 14.5)
    Thymidylate_kin; Thymidylate kinase (PF02223; HMM-score: 14.4)
    T2SSE; Type II/IV secretion system protein (PF00437; HMM-score: 14.3)
    APS_kinase; Adenylylsulphate kinase (PF01583; HMM-score: 14.1)
    AAA_30; AAA domain (PF13604; HMM-score: 13.7)
    AAA_22; AAA domain (PF13401; HMM-score: 13.3)
    NB-ARC; NB-ARC domain (PF00931; HMM-score: 12.5)
    TrwB_AAD_bind; Type IV secretion-system coupling protein DNA-binding domain (PF10412; HMM-score: 12)

Structure, modifications & interactions[edit | edit source]

  • domains:
  • modifications:
  • cofactors:
  • effectors:
  • protein partners:

Localization[edit | edit source]

  • PSORTb: Cytoplasmic
    • Cytoplasmic Score: 9.67
    • Cytoplasmic Membrane Score: 0.01
    • Cellwall Score: 0.15
    • Extracellular Score: 0.17
    • 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): 0.044006
    • TAT(Tat/SPI): 0.0012
    • LIPO(Sec/SPII): 0.033459
  • predicted transmembrane helices (TMHMM): 0

Accession numbers[edit | edit source]

Protein sequence[edit | edit source]

  • MKATTIIGIAGGSGSGKTTVTNEIMKNLEGHSVALLAQDYYYKDQKHLTFDERLETNYDHPFAFDNDLLIENLKDLKNGKAVEVPTYDYASHTRSDITIDFKPKDVIIVEGIFALENKVLRDMMDVKIYVDTDADLRILRRLTRDTKERGRSMDSVINQYLSVVRPMHDQFIEPTKKYADIIIPEGGSNKVAIDIMTTKIQSLVSKQ

Experimental data[edit | edit source]

  • experimentally validated: PeptideAtlas
    experimental localization: Cytoplasmic [1] [2] [3]
    quantitative data / protein copy number per cell: 408 [4]

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: 25.25 h [5]

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. 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)
  2. 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)
  3. 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)
  4. 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)
  5. Stephan Michalik, Jörg Bernhardt, Andreas Otto, Martin Moche, Dörte Becher, Hanna Meyer, Michael Lalk, Claudia Schurmann, Rabea Schlüter, Holger Kock, Ulf Gerth, Michael Hecker
    Life and death of proteins: a case study of glucose-starved Staphylococcus aureus.
    Mol Cell Proteomics: 2012, 11(9);558-70
    [PubMed:22556279] [WorldCat.org] [DOI] (I p)

Relevant publications[edit | edit source]