From AureoWiki
Jump to navigation Jump to search

NCBI: 10-JUN-2013

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus COL
  • locus tag: SACOL1227 [new locus tag: SACOL_RS06285 ]
  • pan locus tag?: SAUPAN003498000
  • symbol: def2
  • pan gene symbol?: def2
  • synonym:
  • product: peptide deformylase

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SACOL1227 [new locus tag: SACOL_RS06285 ]
  • symbol: def2
  • product: peptide deformylase
  • replicon: chromosome
  • strand: +
  • coordinates: 1237405..1237893
  • length: 489
  • 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
    ATGGCGATTAAAAAGTTAGTACCAGCATCGCATCCTATTTTAACGAAAAAAGCGCAAGCA
    GTTAAAACATTTGATGATTCGTTAAAAAGATTATTACAAGATTTAGAAGATACAATGTAT
    GCACAAGAAGCTGCTGGCTTATGTGCACCTCAAATTAATCAGTCATTGCAAGTGGCAATT
    ATTGATATGGAAATGGAAGGATTATTACAACTTGTTAATCCGAAAATTATTAGTCAATCA
    AATGAAACAATAACAGACTTAGAAGGTTCAATTACATTGCCAGATGTTTACGGCGAAGTG
    ACAAGAAGTAAAATGATAGTTGTCGAAAGTTATGACGTCAATGGGAACAAAGTTGAACTA
    ACTGCACATGAAGATGTAGCAAGAATGATTTTGCATATTATAGATCAAATGAACGGTATC
    CCTTTTACAGAACGTGCGGACCGTATTTTAACAGATAAAGAAGTGGAGGCATATTTTATA
    AATGACTAA
    60
    120
    180
    240
    300
    360
    420
    480
    489

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: SACOL1227 [new locus tag: SACOL_RS06285 ]
  • symbol: Def2
  • description: peptide deformylase
  • length: 162
  • theoretical pI: 4.36649
  • theoretical MW: 18101.7
  • GRAVY: -0.110494

⊟Function[edit | edit source]

  • reaction:
    EC 3.5.1.31?  ExPASy
    Formylmethionine deformylase N-formyl-L-methionine + H2O = formate + L-methionine
  • TIGRFAM:
    Genetic information processing Protein fate Protein modification and repair peptide deformylase (TIGR00079; EC 3.5.1.88; HMM-score: 105.4)
  • TheSEED  :
    • Peptide deformylase (EC 3.5.1.88)
    Carbohydrates Central carbohydrate metabolism Dehydrogenase complexes  Peptide deformylase (EC 3.5.1.88)
    and 1 more
    Protein Metabolism Protein biosynthesis Translation termination factors bacterial  Peptide deformylase (EC 3.5.1.88)
  • PFAM:
    no clan defined Pep_deformylase; Polypeptide deformylase (PF01327; HMM-score: 132)
    and 1 more
    4H_Cytokine (CL0053) CNTF; Ciliary neurotrophic factor (PF01110; HMM-score: 12.8)

⊟Structure, modifications & cofactors[edit | edit source]

  • domains:
  • modifications:
  • cofactors:
  • effectors:

⊟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): 0.009408
    • TAT(Tat/SPI): 0.000392
    • LIPO(Sec/SPII): 0.000424
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MAIKKLVPASHPILTKKAQAVKTFDDSLKRLLQDLEDTMYAQEAAGLCAPQINQSLQVAIIDMEMEGLLQLVNPKIISQSNETITDLEGSITLPDVYGEVTRSKMIVVESYDVNGNKVELTAHEDVARMILHIIDQMNGIPFTERADRILTDKEVEAYFIND

⊟Experimental data[edit | edit source]

  • experimentally validated: PeptideAtlas
  • protein localization: Cytoplasmic [1] [2] [3]
  • quantitative data / protein copy number per cell:
  • interaction partners:
    SACOL1760(ackA)acetate kinase  [4] (data from MRSA252)
    SACOL2657(arcA)arginine deiminase  [4] (data from MRSA252)
    SACOL0557(cysK)cysteine synthase  [4] (data from MRSA252)
    SACOL1016(fabI)enoyl-ACP reductase  [4] (data from MRSA252)
    SACOL1072(folD)bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase  [4] (data from MRSA252)
    SACOL0593(fusA)elongation factor G  [4] (data from MRSA252)
    SACOL1734(gapA2)glyceraldehyde 3-phosphate dehydrogenase 2  [4] (data from MRSA252)
    SACOL1922(hemL2)glutamate-1-semialdehyde aminotransferase  [4] (data from MRSA252)
    SACOL1477(ilvA1)threonine dehydratase  [4] (data from MRSA252)
    SACOL0222(ldh1)L-lactate dehydrogenase  [4] (data from MRSA252)
    SACOL2092(murAA)UDP-N-acetylglucosamine 1-carboxyvinyltransferase  [4] (data from MRSA252)
    SACOL0793(nrdF)ribonucleotide-diphosphate reductase subunit beta  [4] (data from MRSA252)
    SACOL1102(pdhA)pyruvate dehydrogenase complex E1 component subunit alpha  [4] (data from MRSA252)
    SACOL1105(pdhD)dihydrolipoamide dehydrogenase  [4] (data from MRSA252)
    SACOL2128(pdp)pyrimidine-nucleoside phosphorylase  [4] (data from MRSA252)
    SACOL0204(pflB)formate acetyltransferase  [4] (data from MRSA252)
    SACOL1745(pyk)pyruvate kinase  [4] (data from MRSA252)
    SACOL0584(rplA)50S ribosomal protein L1  [4] (data from MRSA252)
    SACOL2232(rplP)50S ribosomal protein L16  [4] (data from MRSA252)
    SACOL1274(rpsB)30S ribosomal protein S2  [4] (data from MRSA252)
    SACOL2233(rpsC)30S ribosomal protein S3  [4] (data from MRSA252)
    SACOL2222(rpsE)30S ribosomal protein S5  [4] (data from MRSA252)
    SACOL2230(rpsQ)30S ribosomal protein S17  [4] (data from MRSA252)
    SACOL2057(rsbU)sigma factor B regulator protein  [4] (data from MRSA252)
    SACOL0594(tuf)elongation factor Tu  [4] (data from MRSA252)
    SACOL2104(upp)uracil phosphoribosyltransferase  [4] (data from MRSA252)
    SACOL0731LysR family transcriptional regulator  [4] (data from MRSA252)
    SACOL0834hypothetical protein  [4] (data from MRSA252)
    SACOL0944NADH dehydrogenase  [4] (data from MRSA252)
    SACOL1759universal stress protein  [4] (data from MRSA252)
    SACOL1793hypothetical protein  [4] (data from MRSA252)
    SACOL2293NAD/NADP octopine/nopaline dehydrogenase  [4] (data from MRSA252)
    SACOL2297hypothetical protein  [4] (data from MRSA252)
    SACOL2553pyruvate oxidase  [4] (data from MRSA252)
    SACOL2561hydroxymethylglutaryl-CoA synthase  [4] (data from MRSA252)

⊟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: 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. ↑ 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. ↑ 4.00 4.01 4.02 4.03 4.04 4.05 4.06 4.07 4.08 4.09 4.10 4.11 4.12 4.13 4.14 4.15 4.16 4.17 4.18 4.19 4.20 4.21 4.22 4.23 4.24 4.25 4.26 4.27 4.28 4.29 4.30 4.31 4.32 4.33 4.34 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 | edit source]

Retrieved from "http://aureowiki.med.uni-greifswald.de/index.php?title=SACOL1227&oldid=91136"