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NCBI: 06-JUL-2013

Summary[edit source | edit]

  • organism: Staphylococcus aureus Newman
  • locus tag: NWMN_0960 [new locus tag: NWMN_RS05385 ]
  • pan locus tag?: SAUPAN003318000
  • symbol: phdB
  • pan gene symbol?: pdhB
  • synonym:
  • product: pyruvate dehydrogenase E1 component, beta subunit

Genome View[edit source | edit]

Gene[edit source | edit]

General[edit source | edit]

  • type: CDS
  • locus tag: NWMN_0960 [new locus tag: NWMN_RS05385 ]
  • symbol: phdB
  • product: pyruvate dehydrogenase E1 component, beta subunit
  • replicon: chromosome
  • strand: +
  • coordinates: 1066233..1067210
  • length: 978
  • 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
    ATGGCACAAATGACAATGGTTCAAGCGATTAATGATGCGCTTAAAACTGAACTTAAAAAT
    GACCAAGATGTTTTAATTTTTGGTGAAGACGTTGGTGTTAACGGCGGTGTTTTCCGTGTT
    ACTGAAGGACTACAAAAAGAATTTGGTGAAGATAGAGTATTCGATACACCTTTAGCTGAA
    TCAGGTATTGGTGGTTTAGCGATGGGTCTTGCAGTTGAAGGATTCCGTCCGGTTATGGAA
    GTACAATTCTTAGGTTTCGTATTCGAAGTATTTGATGCGATTGCTGGACAAATTGCACGT
    ACTCGTTTCCGTTCAGGCGGTACTAAAACTGCACCTGTAACAATTCGTAGCCCATTTGGT
    GGTGGCGTACACACACCAGAATTACACGCAGATAACTTAGAAGGTATTTTAGCTCAATCT
    CCAGGTCTAAAGGTTGTTATTCCTTCAGGCCCATACGATGCGAAAGGTTTATTAATTTCT
    TCTATTAGAAGTAATGACCCAGTCGTATACTTAGAGCATATGAAATTGTATCGTTCATTC
    CGTGAAGAAGTACCTGAAGAAGAATATACAATTGACATTGGTAAGGCTAATGTGAAAAAA
    GAAGGTAATGACATTTCAATCATCACATACGGTGCAATGGTTCAAGAATCAATGAAAGCT
    GCAGAAGAACTTGAAAAAGATGGTTATTCTGTTGAAGTAATTGACTTACGTACTGTTCAA
    CCAATCGATGTTGACACAATTGTAGCTTCAGTTGAAAAAACTGGTCGTGCAGTTGTAGTT
    CAAGAAGCACAACGTCAAGCTGGTGTTGGTGCAGCAGTTGTAGCTGAATTAAGTGAACGT
    GCAATCCTTTCATTAGAAGCACCTATTGGAAGAGTTGCAGCAGCAGATACAATTTATCCA
    TTCACTCAAGCTGAAAATGTTTGGTTACCAAACAAAAATGACATCATCGAAAAAGCAAAA
    GAAACTTTAGAATTTTAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    900
    960
    978

Protein[edit source | edit]

General[edit source | edit]

  • locus tag: NWMN_0960 [new locus tag: NWMN_RS05385 ]
  • symbol: PhdB
  • description: pyruvate dehydrogenase E1 component, beta subunit
  • length: 325
  • theoretical pI: 4.36436
  • theoretical MW: 35245.8
  • GRAVY: -0.0467692

Function[edit source | edit]

  • reaction:
  • TIGRFAM:
    MetabolismBiosynthesis of cofactors, prosthetic groups, and carriersOther1-deoxy-D-xylulose-5-phosphate synthase (TIGR00204; EC 2.2.1.7; HMM-score: 83)
    MetabolismBiosynthesis of cofactors, prosthetic groups, and carriersThiamine1-deoxy-D-xylulose-5-phosphate synthase (TIGR00204; EC 2.2.1.7; HMM-score: 83)
    MetabolismBiosynthesis of cofactors, prosthetic groups, and carriersPyridoxine1-deoxy-D-xylulose-5-phosphate synthase (TIGR00204; EC 2.2.1.7; HMM-score: 83)
    2-oxoacid:acceptor oxidoreductase, alpha subunit (TIGR03710; HMM-score: 25.6)
    pyruvate:ferredoxin (flavodoxin) oxidoreductase (TIGR02176; EC 1.2.7.1; HMM-score: 10.5)
  • TheSEED:  
    CarbohydratesCentral carbohydrate metabolismDehydrogenase complexes Pyruvate dehydrogenase E1 component beta subunit (EC 1.2.4.1) 
    Central carbohydrate metabolismPyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate Pyruvate dehydrogenase E1 component beta subunit (EC 1.2.4.1) 
  • PFAM:
    TKC_like (CL0591) Transketolase_C; Transketolase, C-terminal domain (PF02780; HMM-score: 135.3)
    THDP-binding (CL0254) Transket_pyr; Transketolase, pyrimidine binding domain (PF02779; HMM-score: 130.1)
    TKC_like (CL0591) PFOR_II; Pyruvate:ferredoxin oxidoreductase core domain II (PF17147; HMM-score: 18.3)

Structure, modifications & interactions[edit source | edit]

  • domains:
  • modifications:
  • cofactors:
  • effectors:
  • protein partners:
    NWMN_2534(arcA)arginine deiminase  [1] (data from MRSA252)
    NWMN_1587(citC)isocitrate dehydrogenase  [1] (data from MRSA252)
    NWMN_1568(clpX)ATP-dependent protease ATP-binding subunit ClpX  [1] (data from MRSA252)
    NWMN_1483(dnaK)molecular chaperone DnaK  [1] (data from MRSA252)
    NWMN_1096(ftsZ)cell division protein FtsZ  [1] (data from MRSA252)
    NWMN_0509(fus)elongation factor G  [1] (data from MRSA252)
    NWMN_1580(gapB)glyceraldehyde 3-phosphate dehydrogenase 2  [1] (data from MRSA252)
    NWMN_1838(gatA)aspartyl/glutamyl-tRNA amidotransferase subunit A  [1] (data from MRSA252)
    NWMN_1837(gatB)aspartyl/glutamyl-tRNA amidotransferase subunit B  [1] (data from MRSA252)
    NWMN_1348(ilvA)threonine dehydratase  [1] (data from MRSA252)
    NWMN_2004(murA)UDP-N-acetylglucosamine 1-carboxyvinyltransferase  [1] (data from MRSA252)
    NWMN_0961(pdhC)branched-chain alpha-keto acid dehydrogenase subunit E2  [1] (data from MRSA252)
    NWMN_0962(pdhD)dihydrolipoamide dehydrogenase  [1] (data from MRSA252)
    NWMN_0162(pflB)formate acetyltransferase  [1] (data from MRSA252)
    NWMN_0959(phdA)pyruvate dehydrogenase E1 component, alpha subunit  [1] (data from MRSA252)
    NWMN_2438(poxB)pyruvate oxidase  [1] (data from MRSA252)
    NWMN_1592(pykA)pyruvate kinase  [1] (data from MRSA252)
    NWMN_0500(rplA)50S ribosomal protein L1  [1] (data from MRSA252)
    NWMN_2149(rplB)50S ribosomal protein L2  [1] (data from MRSA252)
    NWMN_2152(rplC)50S ribosomal protein L3  [1] (data from MRSA252)
    NWMN_2151(rplD)50S ribosomal protein L4  [1] (data from MRSA252)
    NWMN_2140(rplE)50S ribosomal protein L5  [1] (data from MRSA252)
    NWMN_2133(rplO)50S ribosomal protein L15  [1] (data from MRSA252)
    NWMN_1151(rplS)50S ribosomal protein L19  [1] (data from MRSA252)
    NWMN_1572(rplT)50S ribosomal protein L20  [1] (data from MRSA252)
    NWMN_1549(rplU)50S ribosomal protein L21  [1] (data from MRSA252)
    NWMN_2147(rplV)50S ribosomal protein L22  [1] (data from MRSA252)
    NWMN_2150(rplW)50S ribosomal protein L23  [1] (data from MRSA252)
    NWMN_1166(rpsB)30S ribosomal protein S2  [1] (data from MRSA252)
    NWMN_2146(rpsC)30S ribosomal protein S3  [1] (data from MRSA252)
    NWMN_1613(rpsD)30S ribosomal protein S4  [1] (data from MRSA252)
    NWMN_2135(rpsE)30S ribosomal protein S5  [1] (data from MRSA252)
    NWMN_2143(rpsQ)30S ribosomal protein S17  [1] (data from MRSA252)
    NWMN_1326(sucA)2-oxoglutarate dehydrogenase E1 component  [1] (data from MRSA252)
    NWMN_1325(sucB)dihydrolipoamide succinyltransferase  [1] (data from MRSA252)
    NWMN_0510(tufA)elongation factor Tu  [1] (data from MRSA252)
    NWMN_0355GTP-dependent nucleic acid-binding protein EngD  [1] (data from MRSA252)
    NWMN_0811hypothetical protein  [1] (data from MRSA252)
    NWMN_0839fumarylacetoacetate hydrolase family protein  [1] (data from MRSA252)
    NWMN_1382DNA-binding protein HU  [1] (data from MRSA252)
    NWMN_1604universal stress protein family protein  [1] (data from MRSA252)
    NWMN_2026aldehyde dehydrogenase family protein  [1] (data from MRSA252)
    NWMN_24541-pyrroline-5-carboxylate dehydrogenase  [1] (data from MRSA252)

Localization[edit source | edit]

  • 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
    • Ymax: 0.109
    • Ymax_pos: 16
    • Cmax: 0.127
    • Cmax_pos: 10
    • Smax: 0.167
    • Smax_pos: 9
    • Smean: 0.11
    • D: 0.109
  • predicted transmembrane helices (TMHMM): 0

Accession numbers[edit source | edit]

Protein sequence[edit source | edit]

  • MAQMTMVQAINDALKTELKNDQDVLIFGEDVGVNGGVFRVTEGLQKEFGEDRVFDTPLAESGIGGLAMGLAVEGFRPVMEVQFLGFVFEVFDAIAGQIARTRFRSGGTKTAPVTIRSPFGGGVHTPELHADNLEGILAQSPGLKVVIPSGPYDAKGLLISSIRSNDPVVYLEHMKLYRSFREEVPEEEYTIDIGKANVKKEGNDISIITYGAMVQESMKAAEELEKDGYSVEVIDLRTVQPIDVDTIVASVEKTGRAVVVQEAQRQAGVGAAVVAELSERAILSLEAPIGRVAAADTIYPFTQAENVWLPNKNDIIEKAKETLEF

Experimental data[edit source | edit]

  • experimentally validated: no data available

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: no data available

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 1.40 1.41 1.42 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 source | edit]