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NCBI: 10-JUN-2013

Summary[edit source | edit]

  • organism: Staphylococcus aureus COL
  • locus tag: SACOL0524 [new locus tag: SACOL_RS02675 ]
  • pan locus tag?: SAUPAN002216000
  • symbol: tmk
  • pan gene symbol?: tmk
  • synonym:
  • product: thymidylate kinase

Genome View[edit source | edit]

Gene[edit source | edit]

General[edit source | edit]

  • type: CDS
  • locus tag: SACOL0524 [new locus tag: SACOL_RS02675 ]
  • symbol: tmk
  • product: thymidylate kinase
  • replicon: chromosome
  • strand: +
  • coordinates: 536396..537013
  • length: 618
  • essential: unknown 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
    ATGTCAGCTTTTATAACTTTTGAGGGCCCAGAAGGCTCTGGAAAAACAACTGTAATTAAT
    GAAGTTTACCATAGATTAGTAAAAGATTATGATGTCATTATGACTAGAGAACCAGGTGGT
    GTTCCTACTGGTGAAGAAATACGTAAAATTGTATTAGAAGGCAATGATATGGACATTAGA
    ACTGAAGCAATGTTATTTGCTGCATCTAGAAGAGAACATCTTGTATTAAAGGTCATACCA
    GCTTTAAAAGAAGGTAAGGTTGTGTTGTGTGATCGCTATATCGATAGTTCATTAGCTTAT
    CAAGGTTATGCTAGAGGGATTGGCGTTGAAGAAGTAAGAGCATTAAACGAATTTGCAATA
    AATGGATTATATCCAGACTTGACGATTTATTTAAATGTTAGTGCTGAAGTAGGTCGCGAA
    CGTATTATTAAAAATTCAAGAGATCAAAATAGATTAGATCAAGAAGATTTAAAGTTTCAC
    GAAAAAGTAATTGAAGGTTACCAAGAAATCATTCATAATGAATCACAACGGTTCAAAAGC
    GTTAATGCAGATCAACCTCTTGAAAATGTTGTTGAAGACACGTATCAAACTATCATCAAA
    TATTTAGAAAAGATATGA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    618

Protein[edit source | edit]

Protein Data Bank: 4HDC
Protein Data Bank: 4HEJ

General[edit source | edit]

  • locus tag: SACOL0524 [new locus tag: SACOL_RS02675 ]
  • symbol: Tmk
  • description: thymidylate kinase
  • length: 205
  • theoretical pI: 4.8144
  • theoretical MW: 23424.4
  • GRAVY: -0.379024

Function[edit source | edit]

  • reaction:
    EC 2.7.4.9?  ExPASy
    dTMP kinaseATP + dTMP = ADP + dTDP
  • TIGRFAM:
    MetabolismPurines, pyrimidines, nucleosides, and nucleotidesNucleotide and nucleoside interconversionsdTMP kinase (TIGR00041; EC 2.7.4.9; HMM-score: 188.8)
    putative cytidylate kinase (TIGR02173; EC 2.7.4.14; HMM-score: 20.2)
    MetabolismCentral intermediary metabolismPhosphorus compoundsphosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN (TIGR02322; HMM-score: 16.4)
    MetabolismBiosynthesis of cofactors, prosthetic groups, and carriersMolybdopterinmolybdopterin-guanine dinucleotide biosynthesis protein B (TIGR00176; HMM-score: 15.1)
    adenylate kinase (TIGR01360; EC 2.7.4.3; HMM-score: 14.8)
    MetabolismCentral intermediary metabolismNitrogen metabolismurease accessory protein UreG (TIGR00101; HMM-score: 12.1)
  • TheSEED:  
    Nucleosides and NucleotidesPyrimidinespyrimidine conversions Thymidylate kinase (EC 2.7.4.9) 
    CBSS-393133.3.peg.2787 Thymidylate kinase (EC 2.7.4.9) 
    COG1399 Thymidylate kinase (EC 2.7.4.9) 
  • PFAM:
    P-loop_NTPase (CL0023) Thymidylate_kin; Thymidylate kinase (PF02223; HMM-score: 173.7)
    AAA_28; AAA domain (PF13521; HMM-score: 28.4)
    dNK; Deoxynucleoside kinase (PF01712; HMM-score: 27.3)
    AAA_17; AAA domain (PF13207; HMM-score: 24.7)
    AAA_33; AAA domain (PF13671; HMM-score: 20.4)
    AAA_18; AAA domain (PF13238; HMM-score: 19.8)
    AAA_16; AAA ATPase domain (PF13191; HMM-score: 18.8)
    AAA_22; AAA domain (PF13401; HMM-score: 16.1)
    NB-ARC; NB-ARC domain (PF00931; HMM-score: 15.3)
    ATPase_2; ATPase domain predominantly from Archaea (PF01637; HMM-score: 15.2)
    SKI; Shikimate kinase (PF01202; HMM-score: 14.5)
    T2SSE; Type II/IV secretion system protein (PF00437; HMM-score: 13.6)
    AAA_11; AAA domain (PF13086; HMM-score: 12.7)

Structure, modifications & interactions[edit source | edit]

  • domains:
  • modifications:
  • cofactors:
  • effectors:
  • protein partners:
    SACOL0123(deoC1)deoxyribose-phosphate aldolase  [1] (data from MRSA252)
    SACOL1637(dnaK)molecular chaperone DnaK  [1] (data from MRSA252)
    SACOL1587(efp)elongation factor P  [1] (data from MRSA252)
    SACOL0842(eno)phosphopyruvate hydratase  [1] (data from MRSA252)
    SACOL0988(fabF)3-oxoacyl-ACP synthase  [1] (data from MRSA252)
    SACOL1199(ftsZ)cell division protein FtsZ  [1] (data from MRSA252)
    SACOL0838(gapA1)glyceraldehyde 3-phosphate dehydrogenase  [1] (data from MRSA252)
    SACOL1513(hup)DNA-binding protein HU  [1] (data from MRSA252)
    SACOL1741(icd)isocitrate dehydrogenase  [1] (data from MRSA252)
    SACOL1477(ilvA1)threonine dehydratase  [1] (data from MRSA252)
    SACOL1288(infB)translation initiation factor IF-2  [1] (data from MRSA252)
    SACOL0222(ldh1)L-lactate dehydrogenase  [1] (data from MRSA252)
    SACOL0033(mecA)penicillin-binding protein 2'  [1] (data from MRSA252)
    SACOL2116(murAB)UDP-N-acetylglucosamine 1-carboxyvinyltransferase  [1] (data from MRSA252)
    SACOL1102(pdhA)pyruvate dehydrogenase complex E1 component subunit alpha  [1] (data from MRSA252)
    SACOL1103(pdhB)pyruvate dehydrogenase complex E1 component subunit beta  [1] (data from MRSA252)
    SACOL1104(pdhC)branched-chain alpha-keto acid dehydrogenase E2  [1] (data from MRSA252)
    SACOL1105(pdhD)dihydrolipoamide dehydrogenase  [1] (data from MRSA252)
    SACOL2128(pdp)pyrimidine-nucleoside phosphorylase  [1] (data from MRSA252)
    SACOL0544(prsA)ribose-phosphate pyrophosphokinase  [1] (data from MRSA252)
    SACOL1091(ptsH)phosphocarrier protein HPr  [1] (data from MRSA252)
    SACOL1745(pyk)pyruvate kinase  [1] (data from MRSA252)
    SACOL2236(rplB)50S ribosomal protein L2  [1] (data from MRSA252)
    SACOL2239(rplC)50S ribosomal protein L3  [1] (data from MRSA252)
    SACOL2238(rplD)50S ribosomal protein L4  [1] (data from MRSA252)
    SACOL2224(rplF)50S ribosomal protein L6  [1] (data from MRSA252)
    SACOL0015(rplI)50S ribosomal protein L9  [1] (data from MRSA252)
    SACOL0585(rplJ)50S ribosomal protein L10  [1] (data from MRSA252)
    SACOL0586(rplL)50S ribosomal protein L7/L12  [1] (data from MRSA252)
    SACOL2207(rplM)50S ribosomal protein L13  [1] (data from MRSA252)
    SACOL2220(rplO)50S ribosomal protein L15  [1] (data from MRSA252)
    SACOL2232(rplP)50S ribosomal protein L16  [1] (data from MRSA252)
    SACOL1257(rplS)50S ribosomal protein L19  [1] (data from MRSA252)
    SACOL1725(rplT)50S ribosomal protein L20  [1] (data from MRSA252)
    SACOL1702(rplU)50S ribosomal protein L21  [1] (data from MRSA252)
    SACOL2234(rplV)50S ribosomal protein L22  [1] (data from MRSA252)
    SACOL2237(rplW)50S ribosomal protein L23  [1] (data from MRSA252)
    SACOL0545(rplY)50S ribosomal protein L25/general stress protein Ctc  [1] (data from MRSA252)
    SACOL1274(rpsB)30S ribosomal protein S2  [1] (data from MRSA252)
    SACOL2233(rpsC)30S ribosomal protein S3  [1] (data from MRSA252)
    SACOL1769(rpsD)30S ribosomal protein S4  [1] (data from MRSA252)
    SACOL2222(rpsE)30S ribosomal protein S5  [1] (data from MRSA252)
    SACOL2206(rpsI)30S ribosomal protein S9  [1] (data from MRSA252)
    SACOL1831(tal)translaldolase  [1] (data from MRSA252)
    SACOL1722(tig)trigger factor  [1] (data from MRSA252)
    SACOL0840(tpiA)triosephosphate isomerase  [1] (data from MRSA252)
    SACOL0594(tuf)elongation factor Tu  [1] (data from MRSA252)
    SACOL0521hypothetical protein  [1] (data from MRSA252)
    SACOL0690ABC transporter ATP-binding protein  [1] (data from MRSA252)
    SACOL0731LysR family transcriptional regulator  [1] (data from MRSA252)
    SACOL0944NADH dehydrogenase  [1] (data from MRSA252)
    SACOL1594glycine dehydrogenase subunit 1  [1] (data from MRSA252)
    SACOL1759universal stress protein  [1] (data from MRSA252)
    SACOL1992hypothetical protein  [1] (data from MRSA252)
    SACOL2553pyruvate oxidase  [1] (data from MRSA252)

Localization[edit source | edit]

  • 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
    • Ymax: 0.097
    • Ymax_pos: 45
    • Cmax: 0.131
    • Cmax_pos: 21
    • Smax: 0.116
    • Smax_pos: 40
    • Smean: 0.078
    • D: 0.09
  • predicted transmembrane helices (TMHMM): 0

Accession numbers[edit source | edit]

Protein sequence[edit source | edit]

  • MSAFITFEGPEGSGKTTVINEVYHRLVKDYDVIMTREPGGVPTGEEIRKIVLEGNDMDIRTEAMLFAASRREHLVLKVIPALKEGKVVLCDRYIDSSLAYQGYARGIGVEEVRALNEFAINGLYPDLTIYLNVSAEVGRERIIKNSRDQNRLDQEDLKFHEKVIEGYQEIIHNESQRFKSVNADQPLENVVEDTYQTIIKYLEKI

Experimental data[edit source | edit]

  • experimentally validated: PeptideAtlas
    experimental localization: Cytoplasmic [2] [3] [4]
    quantitative data / protein copy number per cell: 157 [5]

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: 27.64 h [6]

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. 1.00 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 1.33 1.34 1.35 1.36 1.37 1.38 1.39 1.40 1.41 1.42 1.43 1.44 1.45 1.46 1.47 1.48 1.49 1.50 1.51 1.52 1.53 1.54 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)
  6. 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 source | edit]