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NCBI: 10-JUN-2013

Summary[edit source | edit]

  • organism: Staphylococcus aureus COL
  • locus tag: SACOL2095 [new locus tag: SACOL_RS10965 ]
  • pan locus tag?: SAUPAN005394000
  • symbol: atpD
  • pan gene symbol?: atpD
  • synonym:
  • product: F0F1 ATP synthase subunit beta

Genome View[edit source | edit]

Gene[edit source | edit]

General[edit source | edit]

  • type: CDS
  • locus tag: SACOL2095 [new locus tag: SACOL_RS10965 ]
  • symbol: atpD
  • product: F0F1 ATP synthase subunit beta
  • replicon: chromosome
  • strand: -
  • coordinates: 2157139..2158551
  • length: 1413
  • 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
    661
    721
    781
    841
    901
    961
    1021
    1081
    1141
    1201
    1261
    1321
    1381
    ATGGGAATTGGCCGTGTAACTCAAGTTATGGGTCCTGTAATTGATGTTCGATTTGAACAT
    AACGAAGTTCCTAAAATTAATAACGCCTTGGTTATTGATGTGCCTAAAGAAGAAGGTACA
    ATACAACTAACATTAGAAGTTGCGCTGCAATTAGGTGACGACGTTGTTCGTACAATTGCG
    ATGGATTCAACTGATGGTGTCCAAAGAGGCATGGATGTAAAAGATACAGGCAAAGAAATT
    AGTGTACCTGTTGGTGACGAAACATTAGGTCGTGTATTTAATGTACTAGGTGAAACAATT
    GACCTTAAAGAAGAAATTAGTGATTCTGTTCGCCGCGATCCTATCCATCGTCAAGCACCA
    GCATTCGATGAACTTTCAACAGAAGTTCAAATTTTAGAAACAGGTATTAAAGTAGTAGAT
    TTACTAGCACCTTATATTAAAGGTGGTAAAATCGGATTGTTCGGTGGTGCCGGTGTAGGT
    AAAACAGTATTAATCCAAGAATTAATTAACAACATCGCTCAAGAGCACGGTGGTATTTCT
    GTATTCGCCGGTGTAGGTGAACGTACTCGTGAAGGTAACGATTTATACTTCGAAATGAGT
    GACAGTGGTGTAATTAAGAAAACAGCCATGGTATTCGGGCAAATGAATGAGCCACCTGGT
    GCACGTATGCGTGTTGCATTATCTGGTTTAACAATGGCTGAATATTTCCGTGACGAACAA
    GGTCAAGACGTATTATTATTCATCGATAACATTTTCAGATTTACACAAGCTGGTTCTGAG
    GTATCTGCATTATTAGGTCGTATGCCTTCTGCAGTAGGTTACCAACCAACACTTGCTACT
    GAAATGGGACAATTACAAGAACGTATTACGTCTACAACAAAAGGATCAGTTACTTCTATT
    CAAGCGGTATTCGTACCTGCCGATGACTATACTGACCCAGCGCCTGCGACAGCGTTTGCC
    CATTTAGATGCAACTACAAACTTAGAACGTAAATTAACTGAAATGGGTATTTATCCAGCC
    GTGGATCCATTAGCGTCTACATCAAGAGCATTGGAACCATCAATTGTAGGTCAAGAACAT
    TATGAAGTAGCTCGTGATGTACAATCAACACTTCAAAAATACCGTGAATTACAAGATATC
    ATTGCTATCTTAGGTATGGACGAATTATCTGATGAAGATAAACAAACAGTTGAACGCGCA
    CGTAGAATTCAATTCTTCTTATCTCAAAACTTCCACGTAGCGGAACAATTTACTGGTCAA
    AAAGGTTCTTATGTACCTGTTAAGACAACAGTTGCAAACTTTAAAGATATCTTAGATGGT
    AAATATGACCATATTCCAGAAGATGCATTCCGTTTAGTTGGTAGCATGGATGATGTTATT
    GCAAAAGCTAAAGATATGGGTGTTGAAGTATAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    900
    960
    1020
    1080
    1140
    1200
    1260
    1320
    1380
    1413

Protein[edit source | edit]

General[edit source | edit]

  • locus tag: SACOL2095 [new locus tag: SACOL_RS10965 ]
  • symbol: AtpD
  • description: F0F1 ATP synthase subunit beta
  • length: 470
  • theoretical pI: 4.42228
  • theoretical MW: 51399.9
  • GRAVY: -0.161915

Function[edit source | edit]

  • reaction:
    EC 3.6.3.14?  ExPASy
    H+-transporting two-sector ATPaseATP + H2O + H+(In) = ADP + phosphate + H+(Out)
  • TIGRFAM:
    MetabolismEnergy metabolismATP-proton motive force interconversionATP synthase F1, beta subunit (TIGR01039; EC 3.6.3.14; HMM-score: 844.9)
    alternate F1F0 ATPase, F1 subunit beta (TIGR03305; EC 3.6.3.-; HMM-score: 586.7)
    MetabolismEnergy metabolismATP-proton motive force interconversionATPase, FliI/YscN family (TIGR01026; EC 3.6.3.14; HMM-score: 234.1)
    Cellular processesCellular processesPathogenesistype III secretion apparatus H+-transporting two-sector ATPase (TIGR02546; EC 3.6.3.14; HMM-score: 233.1)
    Genetic information processingProtein fateProtein and peptide secretion and traffickingtype III secretion apparatus H+-transporting two-sector ATPase (TIGR02546; EC 3.6.3.14; HMM-score: 233.1)
    Cellular processesCellular processesChemotaxis and motilityflagellar protein export ATPase FliI (TIGR03496; EC 3.6.3.14; HMM-score: 229.2)
    flagellar protein export ATPase FliI (TIGR03498; EC 3.6.3.14; HMM-score: 226.1)
    Cellular processesCellular processesChemotaxis and motilityflagellar protein export ATPase FliI (TIGR03497; EC 3.6.3.14; HMM-score: 216)
    MetabolismEnergy metabolismATP-proton motive force interconversionATP synthase archaeal, B subunit (TIGR01041; EC 3.6.3.14; HMM-score: 143.4)
    MetabolismEnergy metabolismATP-proton motive force interconversionATP synthase archaeal, A subunit (TIGR01043; EC 3.6.3.14; HMM-score: 134.6)
    alternate F1F0 ATPase, F1 subunit alpha (TIGR03324; EC 3.6.3.-; HMM-score: 133.2)
    MetabolismEnergy metabolismATP-proton motive force interconversionATP synthase F1, alpha subunit (TIGR00962; EC 3.6.3.14; HMM-score: 132.4)
    MetabolismTransport and binding proteinsCations and iron carrying compoundsV-type ATPase, A subunit (TIGR01042; EC 3.6.3.14; HMM-score: 121.4)
    MetabolismTransport and binding proteinsCations and iron carrying compoundsV-type ATPase, B subunit (TIGR01040; EC 3.6.3.14; HMM-score: 103)
    Genetic information processingTranscriptionTranscription factorstranscription termination factor Rho (TIGR00767; EC 3.6.4.-; HMM-score: 41.1)
    Genetic information processingProtein synthesisTranslation factorsribosome small subunit-dependent GTPase A (TIGR00157; EC 3.6.-.-; HMM-score: 13)
    Genetic information processingProtein synthesistRNA and rRNA base modificationpseudouridine synthase Rlu family protein, TIGR01621 (TIGR01621; EC 5.4.99.-; HMM-score: 11.9)
  • TheSEED:  
    RespirationATP synthasesF0F1-type ATP synthase ATP synthase beta chain (EC 3.6.3.14) 
  • PFAM:
    P-loop_NTPase (CL0023) ATP-synt_ab; ATP synthase alpha/beta family, nucleotide-binding domain (PF00006; HMM-score: 226.3)
    HAS-barrel (CL0275) ATP-synt_ab_N; ATP synthase alpha/beta family, beta-barrel domain (PF02874; HMM-score: 79.1)
    P-loop_NTPase (CL0023) RsgA_GTPase; RsgA GTPase (PF03193; HMM-score: 23.7)
    AAA; ATPase family associated with various cellular activities (AAA) (PF00004; HMM-score: 19.3)
    ATPase_2; ATPase domain predominantly from Archaea (PF01637; HMM-score: 16.9)
    ABC_tran; ABC transporter (PF00005; HMM-score: 15.8)
    NACHT; NACHT domain (PF05729; HMM-score: 14.9)
    AAA_16; AAA ATPase domain (PF13191; HMM-score: 14.1)
    AAA_19; AAA domain (PF13245; HMM-score: 14)
    RNA_helicase; RNA helicase (PF00910; HMM-score: 13.6)
    ATPase; KaiC (PF06745; HMM-score: 11.9)
    TrwB_AAD_bind; Type IV secretion-system coupling protein DNA-binding domain (PF10412; HMM-score: 10.9)
    NB-ARC; NB-ARC domain (PF00931; HMM-score: 10.9)

Structure, modifications & interactions[edit source | edit]

  • domains:
  • modifications:
  • cofactors:
  • effectors:
  • protein partners:
    SACOL1760(ackA)acetate kinase  [1] (data from MRSA252)
    SACOL0154(aldA1)aldehyde dehydrogenase  [1] (data from MRSA252)
    SACOL2657(arcA)arginine deiminase  [1] (data from MRSA252)
    SACOL1215(carB)carbamoyl phosphate synthase large subunit  [1] (data from MRSA252)
    SACOL1637(dnaK)molecular chaperone DnaK  [1] (data from MRSA252)
    SACOL1329(femC)glutamine synthetase  [1] (data from MRSA252)
    SACOL1072(folD)bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase  [1] (data from MRSA252)
    SACOL1199(ftsZ)cell division protein FtsZ  [1] (data from MRSA252)
    SACOL0593(fusA)elongation factor G  [1] (data from MRSA252)
    SACOL1960(gatB)aspartyl/glutamyl-tRNA amidotransferase subunit B  [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)
    SACOL2623(mqo2)malate:quinone oxidoreductase  [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)
    SACOL0204(pflB)formate acetyltransferase  [1] (data from MRSA252)
    SACOL1745(pyk)pyruvate kinase  [1] (data from MRSA252)
    SACOL2236(rplB)50S ribosomal protein L2  [1] (data from MRSA252)
    SACOL2227(rplE)50S ribosomal protein L5  [1] (data from MRSA252)
    SACOL2224(rplF)50S ribosomal protein L6  [1] (data from MRSA252)
    SACOL0585(rplJ)50S ribosomal protein L10  [1] (data from MRSA252)
    SACOL2232(rplP)50S ribosomal protein L16  [1] (data from MRSA252)
    SACOL1702(rplU)50S ribosomal protein L21  [1] (data from MRSA252)
    SACOL2234(rplV)50S ribosomal protein L22  [1] (data from MRSA252)
    SACOL1274(rpsB)30S ribosomal protein S2  [1] (data from MRSA252)
    SACOL2233(rpsC)30S ribosomal protein S3  [1] (data from MRSA252)
    SACOL2222(rpsE)30S ribosomal protein S5  [1] (data from MRSA252)
    SACOL2214(rpsK)30S ribosomal protein S11  [1] (data from MRSA252)
    SACOL0591(rpsL)30S ribosomal protein S12  [1] (data from MRSA252)
    SACOL1449(sucA)2-oxoglutarate dehydrogenase E1 component  [1] (data from MRSA252)
    SACOL0594(tuf)elongation factor Tu  [1] (data from MRSA252)
    SACOL0564pyridoxal biosynthesis lyase PdxS  [1] (data from MRSA252)
    SACOL0944NADH dehydrogenase  [1] (data from MRSA252)
    SACOL0973fumarylacetoacetate hydrolase  [1] (data from MRSA252)
    SACOL1759universal stress protein  [1] (data from MRSA252)
    SACOL2173alkaline shock protein 23  [1] (data from MRSA252)

Localization[edit source | edit]

  • PSORTb: Cytoplasmic Membrane
    • Cytoplasmic Score: 1.05
    • Cytoplasmic Membrane Score: 8.78
    • Cellwall Score: 0.08
    • Extracellular Score: 0.09
    • 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: 0.12
    • Ymax_pos: 26
    • Cmax: 0.114
    • Cmax_pos: 63
    • Smax: 0.17
    • Smax_pos: 17
    • Smean: 0.106
    • D: 0.115
  • predicted transmembrane helices (TMHMM): 0

Accession numbers[edit source | edit]

Protein sequence[edit source | edit]

  • MGIGRVTQVMGPVIDVRFEHNEVPKINNALVIDVPKEEGTIQLTLEVALQLGDDVVRTIAMDSTDGVQRGMDVKDTGKEISVPVGDETLGRVFNVLGETIDLKEEISDSVRRDPIHRQAPAFDELSTEVQILETGIKVVDLLAPYIKGGKIGLFGGAGVGKTVLIQELINNIAQEHGGISVFAGVGERTREGNDLYFEMSDSGVIKKTAMVFGQMNEPPGARMRVALSGLTMAEYFRDEQGQDVLLFIDNIFRFTQAGSEVSALLGRMPSAVGYQPTLATEMGQLQERITSTTKGSVTSIQAVFVPADDYTDPAPATAFAHLDATTNLERKLTEMGIYPAVDPLASTSRALEPSIVGQEHYEVARDVQSTLQKYRELQDIIAILGMDELSDEDKQTVERARRIQFFLSQNFHVAEQFTGQKGSYVPVKTTVANFKDILDGKYDHIPEDAFRLVGSMDDVIAKAKDMGVEV

Experimental data[edit source | edit]

  • experimentally validated: PeptideAtlas
    experimental localization: Cytoplasmic [2] [3] [4] [5]
    quantitative data / protein copy number per cell: 3923 [6]

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: 23.91 h [7]

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 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, Jan Pané-Farré, Andreas Otto, Susanne Sievers, Michael Hecker, Dörte Becher
    Quantitative cell surface proteome profiling for SigB-dependent protein expression in the human pathogen Staphylococcus aureus via biotinylation approach.
    J. Proteome Res.: 2010, 9(3);1579-90
    [PubMed:20108986] [WorldCat.org] [DOI] (I p)
  4. 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)
  5. 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)
  6. 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)
  7. 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]