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NCBI: 10-JUN-2013

Summary[edit | edit source]

  • organism: Staphylococcus aureus COL
  • locus tag: SACOL1104 [new locus tag: SACOL_RS05640 ]
  • pan locus tag?: SAUPAN003319000
  • symbol: pdhC
  • pan gene symbol?: pdhC
  • synonym:
  • product: branched-chain alpha-keto acid dehydrogenase E2

Genome View[edit | edit source]

Gene[edit | edit source]

General[edit | edit source]

  • type: CDS
  • locus tag: SACOL1104 [new locus tag: SACOL_RS05640 ]
  • symbol: pdhC
  • product: branched-chain alpha-keto acid dehydrogenase E2
  • replicon: chromosome
  • strand: +
  • coordinates: 1114254..1115546
  • length: 1293
  • 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
    GTGGCATTTGAATTTAGATTACCCGATATCGGGGAAGGTATCCACGAAGGTGAAATTGTA
    AAATGGTTTGTTAAAGCTGGAGATACTATTGAAGAAGACGATGTTTTAGCTGAGGTACAA
    AACGATAAATCAGTAGTAGAAATCCCATCACCAGTATCTGGTACTGTAGAAGAAGTTATG
    GTAGAAGAAGGTACAGTAGCTGTAGTTGGTGACGTTATTGTTAAAATCGATGCACCTGAT
    GCAGAAGATATGCAATTTAAAGGTCATGATGATGATTCATCATCTAAAGAAGAACCTGCG
    AAAGAGGAAGCGCCAGCAGAGCAAGCACCTGTAGCTACTCAAACTGAAGAAGTAGATGAA
    AACAGAACTGTTAAAGCAATGCCTTCAGTACGTAAATACGCACGTGAAAAAGGTGTTAAC
    ATTAAAGCAGTTTCTGGATCTGGTAAAAATGGTCGTATTACAAAAGAAGATGTAGATGCA
    TACTTAAATGGTGGTGCACCAACAGCTTCAAATGAATCAGCTGCTTCAGCTACAAGTGAA
    GAAGTTGCTGAAACTCCTGCAGCACCTGCAGCAGTAACATTAGAAGGCGACTTCCCAGAA
    ACAACTGAAAAAATCCCTGCTATGCGTAGAGCAATTGCGAAAGCAATGGTTAACTCTAAG
    CATACTGCACCTCATGTAACATTAATGGATGAAATTGATGTTCAAGCATTATGGGATCAC
    CGTAAGAAATTTAAAGAAATCGCAGCTGAACAAGGTACTAAGTTAACATTCTTACCTTAT
    GTTGTTAAAGCACTTGTTTCTGCATTGAAAAAATACCCAGCACTTAACACTTCATTCAAT
    GAAGAAGCTGGTGAAATCGTTCATAAACATTACTGGAATATCGGTATTGCAGCAGACACT
    GATAGAGGATTATTAGTACCTGTTGTTAAACATGCTGATCGTAAGTCTATTTTCCAAATT
    TCAGATGAAATTAATGAATTAGCTGTTAAAGCACGTGATGGTAAATTAACAGCCGATGAA
    ATGAAAGGTGCTACATGCACAATCAGTAATATCGGTTCAGCTGGTGGACAATGGTTCACT
    CCAGTTATCAATCACCCAGAAGTAGCAATCTTAGGAATTGGCCGTATTGCTCAAAAACCT
    ATCGTTAAAGATGGAGAAATTGTTGCAGCACCAGTATTAGCATTATCATTAAGCTTTGAC
    CACAGACAAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTA
    AATAATCCAGAATTATTATTAATGGAGGGGTAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    900
    960
    1020
    1080
    1140
    1200
    1260
    1293

Protein[edit | edit source]

General[edit | edit source]

  • locus tag: SACOL1104 [new locus tag: SACOL_RS05640 ]
  • symbol: PdhC
  • description: branched-chain alpha-keto acid dehydrogenase E2
  • length: 430
  • theoretical pI: 4.63498
  • theoretical MW: 46382
  • GRAVY: -0.292093

Function[edit | edit source]

  • reaction:
    EC 2.3.1.12?  ExPASy
    Dihydrolipoyllysine-residue acetyltransferase Acetyl-CoA + enzyme N6-(dihydrolipoyl)lysine = CoA + enzyme N6-(S-acetyldihydrolipoyl)lysine
  • TIGRFAM:
    Metabolism Energy metabolism Pyruvate dehydrogenase dihydrolipoyllysine-residue acetyltransferase (TIGR01348; EC 2.3.1.12; HMM-score: 359)
    Metabolism Energy metabolism TCA cycle dihydrolipoyllysine-residue succinyltransferase, E2 component of oxoglutarate dehydrogenase (succinyl-transferring) complex (TIGR01347; EC 2.3.1.61; HMM-score: 310.9)
    2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase (TIGR02927; EC 2.3.1.61; HMM-score: 296.2)
    and 12 more
    Metabolism Energy metabolism Pyruvate dehydrogenase pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase (TIGR01349; EC 2.3.1.12; HMM-score: 274.9)
    Metabolism Transport and binding proteins Other efflux pump membrane protein (TIGR00998; HMM-score: 22.3)
    Metabolism Transport and binding proteins Cations and iron carrying compounds oxaloacetate decarboxylase alpha subunit (TIGR01108; EC 4.1.1.3; HMM-score: 18.4)
    Metabolism Energy metabolism Other oxaloacetate decarboxylase alpha subunit (TIGR01108; EC 4.1.1.3; HMM-score: 18.4)
    Metabolism Fatty acid and phospholipid metabolism Biosynthesis acetyl-CoA carboxylase, biotin carboxyl carrier protein (TIGR00531; HMM-score: 17.3)
    Metabolism Central intermediary metabolism Nitrogen metabolism urea carboxylase (TIGR02712; EC 6.3.4.6; HMM-score: 17.3)
    Metabolism Transport and binding proteins Unknown substrate efflux transporter, RND family, MFP subunit (TIGR01730; HMM-score: 16.5)
    Metabolism Energy metabolism Amino acids and amines glycine cleavage system H protein (TIGR00527; HMM-score: 15.7)
    Metabolism Energy metabolism Glycolysis/gluconeogenesis pyruvate carboxylase (TIGR01235; EC 6.4.1.1; HMM-score: 15.5)
    glycine cleavage protein H-like protein (TIGR03077; HMM-score: 14.9)
    Cellular processes Cellular processes Biosynthesis of natural products NHLM bacteriocin system secretion protein (TIGR03794; HMM-score: 12.2)
    Metabolism Transport and binding proteins Amino acids, peptides and amines NHLM bacteriocin system secretion protein (TIGR03794; HMM-score: 12.2)
  • TheSEED:  
    Carbohydrates Central carbohydrate metabolism Dehydrogenase complexes  Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex (EC 2.3.1.12)
    and 4 more
    Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate  Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex (EC 2.3.1.12)
    Cofactors, Vitamins, Prosthetic Groups, Pigments Lipoic acid BEY LIP  Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex (EC 2.3.1.12)
    Lipoic acid metabolism  Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex (EC 2.3.1.12)
    Lipoate transport  Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex (EC 2.3.1.12)
  • PFAM:
    CoA-acyltrans (CL0149) 2-oxoacid_dh; 2-oxoacid dehydrogenases acyltransferase (catalytic domain) (PF00198; HMM-score: 298.9)
    and 11 more
    Hybrid (CL0105) Biotin_lipoyl; Biotin-requiring enzyme (PF00364; HMM-score: 84.1)
    no clan defined E3_binding; e3 binding domain (PF02817; HMM-score: 62.7)
    Hybrid (CL0105) Biotin_lipoyl_2; Biotin-lipoyl like (PF13533; HMM-score: 40.8)
    GCV_H; Glycine cleavage H-protein (PF01597; HMM-score: 20.5)
    HlyD_3; HlyD family secretion protein (PF13437; HMM-score: 17.7)
    RnfC_N; RnfC Barrel sandwich hybrid domain (PF13375; HMM-score: 17.4)
    no clan defined ATP-synt_ab_Xtn; ATPsynthase alpha/beta subunit N-term extension (PF16886; HMM-score: 15.6)
    Hybrid (CL0105) HlyD_D23; Barrel-sandwich domain of CusB or HlyD membrane-fusion (PF16576; HMM-score: 14.4)
    no clan defined DUF896; Bacterial protein of unknown function (DUF896) (PF05979; HMM-score: 13)
    HTH (CL0123) HTH_17; Helix-turn-helix domain (PF12728; HMM-score: 12.9)
    TIM_barrel (CL0036) DUF2090; Uncharacterized protein conserved in bacteria (DUF2090) (PF09863; HMM-score: 11.9)

Structure, modifications & interactions[edit | edit source]

  • domains:
  • modifications:
  • cofactors: (R)-lipoate
  • effectors:
  • protein partners:

Localization[edit | edit source]

  • PSORTb: Cytoplasmic
    • Cytoplasmic Score: 9.97
    • Cytoplasmic Membrane Score: 0
    • Cellwall Score: 0.01
    • Extracellular Score: 0.02
    • 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): 0.002784
    • TAT(Tat/SPI): 0.000262
    • LIPO(Sec/SPII): 0.000333
  • predicted transmembrane helices (TMHMM): 0

Accession numbers[edit | edit source]

Protein sequence[edit | edit source]

  • MAFEFRLPDIGEGIHEGEIVKWFVKAGDTIEEDDVLAEVQNDKSVVEIPSPVSGTVEEVMVEEGTVAVVGDVIVKIDAPDAEDMQFKGHDDDSSSKEEPAKEEAPAEQAPVATQTEEVDENRTVKAMPSVRKYAREKGVNIKAVSGSGKNGRITKEDVDAYLNGGAPTASNESAASATSEEVAETPAAPAAVTLEGDFPETTEKIPAMRRAIAKAMVNSKHTAPHVTLMDEIDVQALWDHRKKFKEIAAEQGTKLTFLPYVVKALVSALKKYPALNTSFNEEAGEIVHKHYWNIGIAADTDRGLLVPVVKHADRKSIFQISDEINELAVKARDGKLTADEMKGATCTISNIGSAGGQWFTPVINHPEVAILGIGRIAQKPIVKDGEIVAAPVLALSLSFDHRQIDGATGQNAMNHIKRLLNNPELLLMEG

Experimental data[edit | edit source]

  • experimentally validated: PeptideAtlas
    experimental localization: Cytoplasmic [1] [2] [3] [4]
    quantitative data / protein copy number per cell: 6259 [5]

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: 18.99 h [6]

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, 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)
  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 | edit source]