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NCBI: 10-JUN-2013

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus COL
  • locus tag: SACOL1563 [new locus tag: SACOL_RS07960 ]
  • pan locus tag?: SAUPAN004073000
  • symbol: lpdA
  • pan gene symbol?: lpdA
  • synonym:
  • product: dihydrolipoamide dehydrogenase

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SACOL1563 [new locus tag: SACOL_RS07960 ]
  • symbol: lpdA
  • product: dihydrolipoamide dehydrogenase
  • replicon: chromosome
  • strand: -
  • coordinates: 1598534..1599955
  • length: 1422
  • 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
    ATGTCAGAGAAACAATATGATTTAGTCGTTCTCGGTGGAGGTACTGCAGGATATGTTGCT
    GCGATACGTGCGTCTCAATTAGGTAAAAAAGTGGCAATAGTAGAACGACAACTATTAGGA
    GGTACTTGTCTCCATAAAGGTTGTATTCCTACTAAATCGCTGCTTAAATCTGCTGAAGTA
    TTTCAAACAGTAAAACAGGCAGCAATGTTTGGCGTTGATGTCAAAGATGCTAATGTTAAT
    TTTGAAAATATGTTGGCACGAAAAGAAGACATTATTAATCAAATGTATCAAGGTGTAAAG
    CATTTAATGCAACACAATCACATTGACATTTATAATGGCACGGGACGTATTCTAGGTACA
    TCTATATTTTCACCTCAAAGTGGCACAATTTCTGTCGAATATGAAGATGGTGAATCAGAC
    TTATTACCCAACCAATTTGTATTAATTGCAACTGGTTCTTCGCCTGCAGAGTTGCCATTC
    TTATCATTTGATCATGATAAAATTTTATCTAGCGATGATATATTATCATTAAAGACGTTA
    CCATCAAGTATTGGTATTATTGGTGGTGGTGTTATCGGAATGGAATTTGCATCATTGATG
    ATAGATTTAGGTGTTGACGTAACAGTTATAGAAGCAGGTGAAAGAATTTTACCAACTGAA
    AGTAAACAAGCTTCACAACTATTAAAAAAATCATTGTCAGCACGTGGTGTTAAATTCTAT
    GAGGGAATAAAACTTTCTGAAAATGATATAAATGTTAACGAAGATGGTGTTACGTTTGAA
    ATTTCCTCAGACATAATTAAAGTAGATAAAGTGTTGCTATCGATTGGTAGAAAACCTAAC
    ACATCAGATATTGGTTTAAACAACACTAAAATAAAACTTTCAACATCAGGACATATTTTA
    ACGAACGAATTTCAACAAACTGAAGATAAACATATTTATGCAGCTGGTGATTGTATAGGA
    AAATTACAATTGGCACATGTTGGATCAAAAGAAGGTGTTGTGGCTGTTGATCATATGTTT
    GAGGGGAACCCAATCCCAGTAAACTATAACATGATGCCTAAGTGTATTTATTCACAACCT
    GAAATTGCTTCTATCGGTTTAAACATTGAACAAGCAAAGGCAGAGGGAATGAAAGTTAAA
    AGTTTTAAAGTACCATTTAAAGCAATTGGTAAAGCAGTGATTGATAGCCATGACACAAAC
    GAAGGGTATAGCGAAATGGTGATTGATCAATCAACTGAAGAAATTGTGGGTATTAATATG
    ATTGGTCCACATGTAACAGAATTGATTAATGAGGCATCACTGTTACAGTTCATGAATGGC
    TCGGCATTAGAATTAGGACTAACAACACACGCACATCCTTCCATCTCTGAAGTGTTGATG
    GAATTAGGATTGAAAGCAGAAAGTAGAGCTATTCACGTATAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    900
    960
    1020
    1080
    1140
    1200
    1260
    1320
    1380
    1422

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: SACOL1563 [new locus tag: SACOL_RS07960 ]
  • symbol: LpdA
  • description: dihydrolipoamide dehydrogenase
  • length: 473
  • theoretical pI: 5.20012
  • theoretical MW: 51111.3
  • GRAVY: -0.015222

⊟Function[edit | edit source]

  • reaction:
    EC 1.8.1.4?  ExPASy
    Dihydrolipoyl dehydrogenase Protein N6-(dihydrolipoyl)lysine + NAD+ = protein N6-(lipoyl)lysine + NADH
  • TIGRFAM:
    dihydrolipoyl dehydrogenase (TIGR01350; EC 1.8.1.4; HMM-score: 501.1)
    and 44 more
    Cellular processes Cellular processes Detoxification mercury(II) reductase (TIGR02053; EC 1.16.1.1; HMM-score: 313.4)
    Metabolism Energy metabolism Electron transport glutathione-disulfide reductase (TIGR01424; EC 1.8.1.7; HMM-score: 259.8)
    Metabolism Energy metabolism Electron transport glutathione-disulfide reductase (TIGR01421; EC 1.8.1.7; HMM-score: 236.3)
    mycothione reductase (TIGR03452; EC 1.8.1.15; HMM-score: 200.1)
    thioredoxin and glutathione reductase (TIGR01438; EC 1.6.4.-; HMM-score: 178.6)
    trypanothione-disulfide reductase (TIGR01423; EC 1.8.1.12; HMM-score: 154.2)
    Cellular processes Cellular processes Detoxification CoA-disulfide reductase (TIGR03385; EC 1.8.1.14; HMM-score: 72.8)
    Metabolism Central intermediary metabolism Nitrogen metabolism nitrite reductase [NAD(P)H], large subunit (TIGR02374; EC 1.7.1.4; HMM-score: 65.5)
    Metabolism Energy metabolism Electron transport thioredoxin-disulfide reductase (TIGR01292; EC 1.8.1.9; HMM-score: 50.8)
    pyridine nucleotide-disulfide oxidoreductase family protein (TIGR03169; HMM-score: 50.7)
    Cellular processes Cellular processes Detoxification alkyl hydroperoxide reductase subunit F (TIGR03140; EC 1.8.1.-; HMM-score: 37.9)
    Cellular processes Cellular processes Adaptations to atypical conditions alkyl hydroperoxide reductase subunit F (TIGR03140; EC 1.8.1.-; HMM-score: 37.9)
    mycofactocin system FadH/OYE family oxidoreductase 2 (TIGR03997; EC 1.-.-.-; HMM-score: 34)
    putative alkyl hydroperoxide reductase F subunit (TIGR03143; EC 1.6.4.-; HMM-score: 33.9)
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Chlorophyll and bacteriochlorphyll geranylgeranyl reductase family (TIGR02032; EC 1.3.1.-; HMM-score: 30.6)
    Metabolism Amino acid biosynthesis Glutamate family glutamate synthase (NADPH), homotetrameric (TIGR01316; EC 1.4.1.13; HMM-score: 30.2)
    Metabolism Energy metabolism Anaerobic glycerol-3-phosphate dehydrogenase, anaerobic, B subunit (TIGR03378; EC 1.1.5.3; HMM-score: 27.7)
    Unknown function Enzymes of unknown specificity flavoprotein, HI0933 family (TIGR00275; HMM-score: 25.5)
    Metabolism Energy metabolism Amino acids and amines alanine dehydrogenase (TIGR00518; EC 1.4.1.1; HMM-score: 25)
    glutamate synthase, small subunit (TIGR01318; HMM-score: 25)
    glutamate synthase, NADH/NADPH, small subunit (TIGR01317; EC 1.4.1.-; HMM-score: 23.7)
    Cell structure Cell envelope Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides UDP-galactopyranose mutase (TIGR00031; EC 5.4.99.9; HMM-score: 22.5)
    Metabolism Energy metabolism Amino acids and amines sarcosine oxidase, alpha subunit family (TIGR01372; HMM-score: 20.2)
    FAD dependent oxidoreductase TIGR03364 (TIGR03364; HMM-score: 19.1)
    mycofactocin system FadH/OYE family oxidoreductase 1 (TIGR03996; EC 1.-.-.-; HMM-score: 19)
    Unknown function Enzymes of unknown specificity putative bacillithiol system oxidoreductase, YpdA family (TIGR04018; EC 1.8.-.-; HMM-score: 18.4)
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Menaquinone and ubiquinone 2-polyprenyl-6-methoxyphenol 4-hydroxylase (TIGR01984; EC 1.14.13.-; HMM-score: 17.3)
    squalene-associated FAD-dependent desaturase (TIGR03467; HMM-score: 17.1)
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Thiamine glycine oxidase ThiO (TIGR02352; EC 1.4.3.19; HMM-score: 16.8)
    Metabolism Energy metabolism TCA cycle succinate dehydrogenase, flavoprotein subunit (TIGR01816; HMM-score: 15.5)
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Menaquinone and ubiquinone ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family (TIGR01988; EC 1.14.13.-; HMM-score: 15.2)
    Metabolism Energy metabolism Electron transport flavocytochrome c (TIGR01813; HMM-score: 14.6)
    Genetic information processing Protein synthesis tRNA and rRNA base modification tRNA U-34 5-methylaminomethyl-2-thiouridine biosynthesis protein MnmC, C-terminal domain (TIGR03197; HMM-score: 14.2)
    nucleotide sugar dehydrogenase (TIGR03026; HMM-score: 13.1)
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Chlorophyll and bacteriochlorphyll geranylgeranyl reductase (TIGR02023; EC 1.3.1.-; HMM-score: 12.9)
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Other C-3',4' desaturase CrtD (TIGR02733; EC 1.3.99.-; HMM-score: 12.7)
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Heme, porphyrin, and cobalamin precorrin 3B synthase CobZ (TIGR02485; HMM-score: 11.8)
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Thiamine thiazole biosynthesis enzyme (TIGR00292; HMM-score: 11.2)
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Pyridine nucleotides L-aspartate oxidase (TIGR00551; EC 1.4.3.16; HMM-score: 10.7)
    Metabolism Energy metabolism TCA cycle succinate dehydrogenase or fumarate reductase, flavoprotein subunit (TIGR01812; HMM-score: 10)
    Metabolism Energy metabolism Anaerobic succinate dehydrogenase or fumarate reductase, flavoprotein subunit (TIGR01812; HMM-score: 10)
    Metabolism Energy metabolism Aerobic succinate dehydrogenase or fumarate reductase, flavoprotein subunit (TIGR01812; HMM-score: 10)
    lycopene cyclase family protein (TIGR01790; HMM-score: 8)
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Other phytoene desaturase (TIGR02734; EC 1.14.99.-; HMM-score: 6.7)
  • TheSEED  :
    • Dihydrolipoamide dehydrogenase of branched-chain alpha-keto acid dehydrogenase (EC 1.8.1.4)
    Amino Acids and Derivatives Branched-chain amino acids Isoleucine degradation  Dihydrolipoamide dehydrogenase of branched-chain alpha-keto acid dehydrogenase (EC 1.8.1.4)
    and 2 more
    Amino Acids and Derivatives Branched-chain amino acids Valine degradation  Dihydrolipoamide dehydrogenase of branched-chain alpha-keto acid dehydrogenase (EC 1.8.1.4)
    Carbohydrates Central carbohydrate metabolism Dehydrogenase complexes  Dihydrolipoamide dehydrogenase of branched-chain alpha-keto acid dehydrogenase (EC 1.8.1.4)
  • PFAM:
    NADP_Rossmann (CL0063) Pyr_redox_2; Pyridine nucleotide-disulphide oxidoreductase (PF07992; HMM-score: 200.5)
    and 18 more
    Reductase_C (CL0608) Pyr_redox_dim; Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain (PF02852; HMM-score: 101.2)
    NADP_Rossmann (CL0063) Pyr_redox; Pyridine nucleotide-disulphide oxidoreductase (PF00070; HMM-score: 70.2)
    FAD_oxidored; FAD dependent oxidoreductase (PF12831; HMM-score: 35.1)
    GIDA; Glucose inhibited division protein A (PF01134; HMM-score: 33.9)
    NAD_binding_8; NAD(P)-binding Rossmann-like domain (PF13450; HMM-score: 33)
    Pyr_redox_3; Pyridine nucleotide-disulphide oxidoreductase (PF13738; HMM-score: 32.7)
    AlaDh_PNT_C; Alanine dehydrogenase/PNT, C-terminal domain (PF01262; HMM-score: 31.7)
    DAO; FAD dependent oxidoreductase (PF01266; HMM-score: 28.3)
    HI0933_like; HI0933-like protein (PF03486; HMM-score: 25)
    FAD_binding_2; FAD binding domain (PF00890; HMM-score: 24.6)
    3HCDH_N; 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain (PF02737; HMM-score: 24.3)
    FAD_binding_3; FAD binding domain (PF01494; HMM-score: 19.4)
    Trp_halogenase; Tryptophan halogenase (PF04820; HMM-score: 17.6)
    2-Hacid_dh_C; D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain (PF02826; HMM-score: 17)
    NAD_binding_7; Putative NAD(P)-binding (PF13241; HMM-score: 16.4)
    Thi4; Thi4 family (PF01946; HMM-score: 14.9)
    Lycopene_cycl; Lycopene cyclase protein (PF05834; HMM-score: 13.1)
    TrkA_N; TrkA-N domain (PF02254; HMM-score: 11.4)

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

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

⊟Localization[edit | edit source]

  • PSORTb: Cytoplasmic
    • Cytoplasmic Score: 9.67
    • Cytoplasmic Membrane Score: 0.01
    • Cellwall Score: 0.15
    • Extracellular Score: 0.17
    • 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): 0.021285
    • TAT(Tat/SPI): 0.013625
    • LIPO(Sec/SPII): 0.006558
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MSEKQYDLVVLGGGTAGYVAAIRASQLGKKVAIVERQLLGGTCLHKGCIPTKSLLKSAEVFQTVKQAAMFGVDVKDANVNFENMLARKEDIINQMYQGVKHLMQHNHIDIYNGTGRILGTSIFSPQSGTISVEYEDGESDLLPNQFVLIATGSSPAELPFLSFDHDKILSSDDILSLKTLPSSIGIIGGGVIGMEFASLMIDLGVDVTVIEAGERILPTESKQASQLLKKSLSARGVKFYEGIKLSENDINVNEDGVTFEISSDIIKVDKVLLSIGRKPNTSDIGLNNTKIKLSTSGHILTNEFQQTEDKHIYAAGDCIGKLQLAHVGSKEGVVAVDHMFEGNPIPVNYNMMPKCIYSQPEIASIGLNIEQAKAEGMKVKSFKVPFKAIGKAVIDSHDTNEGYSEMVIDQSTEEIVGINMIGPHVTELINEASLLQFMNGSALELGLTTHAHPSISEVLMELGLKAESRAIHV

⊟Experimental data[edit | edit source]

  • experimentally validated: PeptideAtlas
  • protein localization: Cytoplasmic [1] [2] [3]
  • quantitative data / protein copy number per cell: 115 [4]
  • interaction partners:
    SACOL1741(icd)isocitrate dehydrogenase  [5] (data from MRSA252)
    SACOL1102(pdhA)pyruvate dehydrogenase complex E1 component subunit alpha  [5] (data from MRSA252)
    SACOL1745(pyk)pyruvate kinase  [5] (data from MRSA252)
    SACOL2222(rpsE)30S ribosomal protein S5  [5] (data from MRSA252)
    SACOL15602-oxoisovalerate dehydrogenase, E2 component, dihydrolipoamide acetyltransferase  [5] (data from MRSA252)
    SACOL15622-oxoisovalerate dehydrogenase, E1 component subunit alpha  [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: 14.09 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, 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. ↑ 5.0 5.1 5.2 5.3 5.4 5.5 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)
  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]

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