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NCBI: 10-JUN-2013

Summary[edit source | edit]

  • organism: Staphylococcus aureus COL
  • locus tag: SACOL1431 [new locus tag: SACOL_RS07290 ]
  • pan locus tag?: SAUPAN003809000
  • symbol: dapB
  • pan gene symbol?: dapB
  • synonym:
  • product: dihydrodipicolinate reductase

Genome View[edit source | edit]

Gene[edit source | edit]

General[edit source | edit]

  • type: CDS
  • locus tag: SACOL1431 [new locus tag: SACOL_RS07290 ]
  • symbol: dapB
  • product: dihydrodipicolinate reductase
  • replicon: chromosome
  • strand: +
  • coordinates: 1443745..1444467
  • length: 723
  • 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
    GTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAACGCGTTGCTAGATTAGCAGAA
    GAAAAAGGACATGAAATCGTTGGGGTCATTGAAAATACACCGAAAGCAACAACGCCATAT
    CAACAATATCAACATATTGCAGATGTTAAAGGTGCCGATGTTGCAATAGATTTTTCAAAT
    CCAAATCTGCTTTTCCCTTTATTAGATGAAGATTTTCATTTGCCATTAGTTGTGGCAACA
    ACTGGCGAGAAAGAAAAACTACTTAATAAGTTAGATGAATTGAGTCAAAATATGCCTGTG
    TTTTTCAGCGCGAACATGAGTTATGGCGTTCATGCATTGACTAAAATTTTAGCAGCTGCT
    GTTCCCCTACTTGATGATTTCGACATCGAATTGACTGAGGCACATCATAATAAAAAAGTA
    GATGCACCAAGTGGTACGTTAGAAAAATTGTATGATGTGATCGTATCTTTGAAAGAAAAT
    GTAACACCTGTGTATGATAGACATGAATTAAATGAAAAACGCCAGCCACAAGATATTGGT
    ATACATTCTATTCGTGGAGGTACGATTGTCGGTGAACATGAAGTTCTATTTGCTGGCACT
    GATGAAACGATTCAAATCACGCATCGTGCACAATCAAAAGATATTTTTGCGAATGGTGCA
    ATACAAGCAGCAGAACGCTTAGTTAATAAACCAAACGGCTTTTATACGTTTGACAACTTA
    TAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    723

Protein[edit source | edit]

Protein Data Bank: 3QY9

General[edit source | edit]

  • locus tag: SACOL1431 [new locus tag: SACOL_RS07290 ]
  • symbol: DapB
  • description: dihydrodipicolinate reductase
  • length: 240
  • theoretical pI: 5.13738
  • theoretical MW: 26654.1
  • GRAVY: -0.2225

Function[edit source | edit]

  • reaction:
    EC 1.3.1.26?  ExPASy
    Transferred entry: 1.17.1.8
    EC 1.17.1.8?  ExPASy
    4-hydroxy-tetrahydrodipicolinate reductase(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NAD(P)+ + H2O = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NAD(P)H
  • TIGRFAM:
    MetabolismAmino acid biosynthesisAspartate family4-hydroxy-tetrahydrodipicolinate reductase (TIGR00036; EC 1.17.1.8; HMM-score: 165.6)
    MetabolismAmino acid biosynthesisAspartate familydihydrodipicolinate reductase (TIGR02130; EC 1.17.1.8; HMM-score: 24.2)
    MetabolismEnergy metabolismPentose phosphate pathway6-phosphogluconate dehydrogenase (decarboxylating) (TIGR00872; EC 1.1.1.44; HMM-score: 14.8)
  • TheSEED:  
    Amino Acids and DerivativesLysine, threonine, methionine, and cysteineLysine Biosynthesis DAP Pathway 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) 
  • PFAM:
    NADP_Rossmann (CL0063) DapB_C; Dihydrodipicolinate reductase, C-terminus (PF05173; HMM-score: 130.2)
    DapB_N; Dihydrodipicolinate reductase, N-terminus (PF01113; HMM-score: 56.2)
    F420_oxidored; NADP oxidoreductase coenzyme F420-dependent (PF03807; HMM-score: 12.9)
    TPR (CL0020) Cse1; Cse1 (PF08506; HMM-score: 12.4)

Structure, modifications & interactions[edit source | edit]

  • domains:
  • modifications:
  • cofactors:
  • effectors:
  • protein partners:

Localization[edit source | edit]

  • 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
    • Ymax: 0.207
    • Ymax_pos: 20
    • Cmax: 0.192
    • Cmax_pos: 20
    • Smax: 0.37
    • Smax_pos: 18
    • Smean: 0.199
    • D: 0.204
  • predicted transmembrane helices (TMHMM): 0

Accession numbers[edit source | edit]

Protein sequence[edit source | edit]

  • MKILLIGYGAMNQRVARLAEEKGHEIVGVIENTPKATTPYQQYQHIADVKGADVAIDFSNPNLLFPLLDEDFHLPLVVATTGEKEKLLNKLDELSQNMPVFFSANMSYGVHALTKILAAAVPLLDDFDIELTEAHHNKKVDAPSGTLEKLYDVIVSLKENVTPVYDRHELNEKRQPQDIGIHSIRGGTIVGEHEVLFAGTDETIQITHRAQSKDIFANGAIQAAERLVNKPNGFYTFDNL

Experimental data[edit source | edit]

  • experimentally validated: PeptideAtlas
    experimental localization: Cytoplasmic [1] [2] [3]
    quantitative data / protein copy number per cell: 958 [4]

Expression & Regulation[edit source | edit]

Operon[edit source | edit]

Regulation[edit source | edit]

  • sigma factor:
  • regulator: CodY
    CodY (TF) important in Amino acid metabolism  RegPrecise    transcription unit transferred from N315 data RegPrecise

Transcription pattern[edit source | edit]

Protein synthesis (provided by Aureolib)[edit source | edit]

Protein stability[edit source | edit]

  • half-life: 18.87 h [5]

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. 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. 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]

Tavarekere S Girish, Vikas Navratna, B Gopal
Structure and nucleotide specificity of Staphylococcus aureus dihydrodipicolinate reductase (DapB).
FEBS Lett.: 2011, 585(16);2561-7
[PubMed:21803042] [WorldCat.org] [DOI] (I p)