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NCBI: 10-JUN-2013

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus COL
  • locus tag: SACOL1312 [new locus tag: SACOL_RS06690 ]
  • pan locus tag?: SAUPAN003596000
  • symbol: miaB
  • pan gene symbol?: miaB
  • synonym:
  • product: (dimethylallyl)adenosine tRNA methylthiotransferase

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SACOL1312 [new locus tag: SACOL_RS06690 ]
  • symbol: miaB
  • product: (dimethylallyl)adenosine tRNA methylthiotransferase
  • replicon: chromosome
  • strand: +
  • coordinates: 1327724..1329268
  • length: 1545
  • 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
    661
    721
    781
    841
    901
    961
    1021
    1081
    1141
    1201
    1261
    1321
    1381
    1441
    1501
    GTGAACGAAGAACAAAGAAAAGCAAGTTCTGTAGATGTTTTAGCTGAGAGAGATAAGAAA
    GCAGAAAAAGATTATAGTAAATATTTTGAACATGTTTATCAGCCGCCTAATTTAAAAGAA
    GCGAAAAAAAGAGGTAAACAAGAAGTTCGTTATAATAGAGATTTCCAAATTGATGAAAAA
    TATCGCGGTATGGGGAACGAGCGTACATTTTTAATTAAAACATATGGATGTCAAATGAAT
    GCACATGACACTGAGGTCATTGCTGGTATACTTGAAGCATTAGGCTATCAAGCAACGACT
    GATATTAACACTGCAGATGTTATTTTAATTAATACATGTGCGATTAGAGAAAATGCCGAG
    AACAAAGTGTTTAGTGAAATAGGTAATTTGAAGCATTTGAAAAAAGAACGACCTGATATT
    TTAATCGGTGTTTGTGGTTGTATGTCACAAGAAGAGTCAGTAGTGAATAAAATTTTAAAA
    TCGTATCAAAATGTAGATATGATATTTGGTACACATAATATTCATCATTTACCAGAAATT
    TTAGAAGAAGCATACTTATCTAAAGCAATGGTTGTTGAAGTATGGTCTAAAGAAGGAGAC
    GTTATTGAAAATCTTCCAAAAGTCCGTGAAGGCAACATTAAAGCATGGGTCAATATTATG
    TATGGTTGTGATAAGTTTTGTACATATTGTATTGTTCCATTTACAAGAGGTAAAGAACGA
    AGCCGTAGACCTGAAGACATTATAGATGAAGTACGTGAACTTGCTCGTGAAGGTTACAAA
    GAAATAACGCTTTTAGGTCAAAATGTAAATTCTTATGGTAAAGATTTACAGGATATAGAA
    TATGACTTAGGAGATCTTTTACAAGCAATTTCTAAAATAGCGATTCCAAGAGTTCGTTTC
    ACAACAAGTCATCCTTGGGACTTTACAGATCACATGATTGATGTTATTTCAGAGGGTGGT
    AATATCGTTCCGCATATCCACTTGCCAGTTCAATCTGGAAATAATGCAGTATTAAAAATA
    ATGGGTAGAAAATATACACGAGAAAGTTATTTGGATTTAGTAAAACGAATCAAAGATAGA
    ATTCCTAATGTAGCATTAACTACAGATATTATTGTAGGGTATCCAAATGAATCAGAGGAA
    CAATTTGAAGAAACTTTAACTCTGTATGATGAAGTTGGTTTTGAACATGCATATACGTAC
    TTGTATTCACAACGTGATGGTACGCCTGCTGCTAAAATGAAAGATAATGTACCTTTAAAT
    GTCAAAAAGGAACGATTGCAACGTTTGAATAAAAAAGTTGGTCATTATTCACAAATAGCT
    ATGAGTAAGTACGAAGGACAAACTGTAACAGTACTTTGTGAAGGAAGTAGTAAAAAAGAT
    GATCAGGTTCTTGCTGGCTACACTGATAAAAATAAGCTAGTTAATTTCAAAGCGCCTAAA
    GAAATGATTGGTAAACTAGTGGAAGTACGAATAGATGAAGCTAAACAGTATTCATTAAAT
    GGCAGTTTTATAAAGGAAGTAGAGCCGGAAATGGTGATTCAATAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    900
    960
    1020
    1080
    1140
    1200
    1260
    1320
    1380
    1440
    1500
    1545

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: SACOL1312 [new locus tag: SACOL_RS06690 ]
  • symbol: MiaB
  • description: (dimethylallyl)adenosine tRNA methylthiotransferase
  • length: 514
  • theoretical pI: 6.26459
  • theoretical MW: 58930.8
  • GRAVY: -0.545914

⊟Function[edit | edit source]

  • reaction:
    EC 2.8.4.3?  ExPASy
    tRNA-2-methylthio-N6-dimethylallyladenosine synthase N6-dimethylallyladenine37 in tRNA + sulfur-(sulfur carrier) + 2 S-adenosyl-L-methionine + reduced electron acceptor = 2-methylthio-N6-dimethylallyladenine37 in tRNA + S-adenosyl-L-homocysteine + (sulfur carrier) + L-methionine + 5'-deoxyadenosine + electron acceptor
  • TIGRFAM:
    Genetic information processing Protein synthesis tRNA and rRNA base modification tRNA-i(6)A37 thiotransferase enzyme MiaB (TIGR01574; EC 2.-.-.-; HMM-score: 630.8)
    radical SAM methylthiotransferase, MiaB/RimO family (TIGR00089; EC 2.1.1.-,2.8.1.-; HMM-score: 528)
    and 16 more
    Genetic information processing Protein synthesis tRNA and rRNA base modification MiaB-like tRNA modifying enzyme (TIGR01579; HMM-score: 334.6)
    Genetic information processing Protein synthesis Ribosomal proteins: synthesis and modification ribosomal protein S12 methylthiotransferase RimO (TIGR01125; EC 2.1.1.-,2.8.1.-; HMM-score: 284.3)
    Genetic information processing Protein synthesis tRNA and rRNA base modification MiaB-like tRNA modifying enzyme, archaeal-type (TIGR01578; HMM-score: 261.7)
    Unknown function Enzymes of unknown specificity B12-binding domain/radical SAM domain protein, MJ_0865 family (TIGR04014; HMM-score: 82.7)
    Unknown function Enzymes of unknown specificity B12-binding domain/radical SAM domain protein, MJ_1487 family (TIGR04013; HMM-score: 63.1)
    Cellular processes Cellular processes Toxin production and resistance radical SAM P-methyltransferase, PhpK family (TIGR04479; EC 2.1.-.-; HMM-score: 40)
    hopanoid biosynthesis associated radical SAM protein HpnJ (TIGR03471; HMM-score: 29.5)
    putative heme utilization radical SAM enzyme HutW (TIGR04107; HMM-score: 29.3)
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Heme, porphyrin, and cobalamin coproporphyrinogen dehydrogenase HemZ (TIGR03994; EC 1.3.99.22; HMM-score: 22.7)
    Unknown function Enzymes of unknown specificity radical SAM protein, TIGR01212 family (TIGR01212; HMM-score: 22.6)
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Heme, porphyrin, and cobalamin putative oxygen-independent coproporphyrinogen III oxidase (TIGR00539; EC 1.3.99.22; HMM-score: 15.4)
    putative variant cofactor biosynthesis B12-binding domain/radical SAM domain protein 1 (TIGR04385; HMM-score: 14.2)
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Heme, porphyrin, and cobalamin oxygen-independent coproporphyrinogen III oxidase (TIGR00538; EC 1.3.99.22; HMM-score: 13.9)
    Cellular processes Cellular processes Toxin production and resistance tryptophan 2-C-methyltransferase (TIGR04428; EC 2.1.1.106; HMM-score: 13.2)
    Unknown function Enzymes of unknown specificity uncharacterized radical SAM protein YgiQ (TIGR03904; HMM-score: 12.9)
    magnesium-protoporphyrin IX monomethyl ester anaerobic oxidative cyclase (TIGR02026; HMM-score: 11.7)
  • TheSEED  :
    • tRNA-i(6)A37 methylthiotransferase
    Protein Metabolism Protein processing and modification Ribosomal protein S12p Asp methylthiotransferase  tRNA-i(6)A37 methylthiotransferase
    and 3 more
    RNA Metabolism RNA processing and modification Methylthiotransferases  tRNA-i(6)A37 methylthiotransferase
    RNA Metabolism RNA processing and modification tRNA modification Archaea  tRNA-i(6)A37 methylthiotransferase
    RNA Metabolism RNA processing and modification tRNA processing  tRNA-i(6)A37 methylthiotransferase
  • PFAM:
    TIM_barrel (CL0036) Radical_SAM; Radical SAM superfamily (PF04055; HMM-score: 118.2)
    CheY (CL0304) UPF0004; Uncharacterized protein family UPF0004 (PF00919; HMM-score: 106.4)
    and 2 more
    OB (CL0021) TRAM; TRAM domain (PF01938; HMM-score: 46)
    TRAM_2; TRAM domain (PF18693; HMM-score: 19.4)

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

  • domains:
  • modifications:
  • cofactors: [4Fe-4S] cluster
  • 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
  • DeepLocPro: Cytoplasmic
    • Cytoplasmic Score: 0.9607
    • Cytoplasmic Membrane Score: 0.0144
    • Cell wall & surface Score: 0.0002
    • Extracellular Score: 0.0247
  • 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): 0.009083
    • TAT(Tat/SPI): 0.002069
    • LIPO(Sec/SPII): 0.003372
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MNEEQRKASSVDVLAERDKKAEKDYSKYFEHVYQPPNLKEAKKRGKQEVRYNRDFQIDEKYRGMGNERTFLIKTYGCQMNAHDTEVIAGILEALGYQATTDINTADVILINTCAIRENAENKVFSEIGNLKHLKKERPDILIGVCGCMSQEESVVNKILKSYQNVDMIFGTHNIHHLPEILEEAYLSKAMVVEVWSKEGDVIENLPKVREGNIKAWVNIMYGCDKFCTYCIVPFTRGKERSRRPEDIIDEVRELAREGYKEITLLGQNVNSYGKDLQDIEYDLGDLLQAISKIAIPRVRFTTSHPWDFTDHMIDVISEGGNIVPHIHLPVQSGNNAVLKIMGRKYTRESYLDLVKRIKDRIPNVALTTDIIVGYPNESEEQFEETLTLYDEVGFEHAYTYLYSQRDGTPAAKMKDNVPLNVKKERLQRLNKKVGHYSQIAMSKYEGQTVTVLCEGSSKKDDQVLAGYTDKNKLVNFKAPKEMIGKLVEVRIDEAKQYSLNGSFIKEVEPEMVIQ

⊟Experimental data[edit | edit source]

  • experimentally validated: PeptideAtlas
  • protein localization: Cytoplasmic [1] [2] [3]
  • quantitative data / protein copy number per cell: 63 [4]
  • interaction partners:
    SACOL0594(tuf)elongation factor Tu  [5] (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. ↑ 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. ↑ 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]

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