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NCBI: 10-JUN-2013

Summary[edit source | edit]

  • organism: Staphylococcus aureus COL
  • locus tag: SACOL1593 [new locus tag: SACOL_RS08115 ]
  • pan locus tag?: SAUPAN004112000
  • symbol: SACOL1593
  • pan gene symbol?: gcvPB
  • synonym:
  • product: glycine dehydrogenase subunit 2

Genome View[edit source | edit]

Gene[edit source | edit]

General[edit source | edit]

  • type: CDS
  • locus tag: SACOL1593 [new locus tag: SACOL_RS08115 ]
  • symbol: SACOL1593
  • product: glycine dehydrogenase subunit 2
  • replicon: chromosome
  • strand: -
  • coordinates: 1625947..1627419
  • length: 1473
  • 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
    1441
    ATGACTAGTAAATCAAGTCCATTAATTTTTGAAAGATCTCGTGAAGGCAGATATGCATAT
    TCATTACCAAAAAGTGATATTAAAACAAATTCTGTTGAGTCATTGTTAGATGATAAATTT
    ATTCGTAAAAACAAAGCGGAGTTTCCTGAAGTTGCTGAACTAGACTTAGTACGTCATTAT
    ACTGAACTTTCAAATAAAAATTTCGGTGTAGACAACGGATTTTATCCATTGGGTTCATGT
    ACGATGAAGTATAACCCTAAAATTAATGAAAAGGTTGCTAGAATACCAGGATTTAGTGAA
    TCACATCCATTACAAGATGAAGATCAAGTTCAAGGTTCATTAGAAATTATTTATAGTTTG
    CAAGAAGAATTAAAAGAAATTACTGGTATGGATGAGGTGACATTACAACCAGCTGCTGGC
    GCACATGGTGAATGGACTGCATTGATGATATTTAAAGCTTACCATGAGAATAATGGTGAA
    GGTCATCGTGATGAAGTCATTGTGCCAGATTCTGCGCATGGTACGAATCCAGCCTCAGCT
    TCATTTGCAGGATTTAAATCAGTTACTGTAAAATCAAACGAACGTGGCGAAGTTAATATT
    GATGACTTGAAACGTGTTGTAAATGAAAATACAGCAGCTATTATGTTAACTAATCCAAAC
    ACTTTAGGTATTTTCGAAAAAAATATTATGGAAATCCGTGAAATCGTCCATAATGCTGGT
    GGTCTATTATATTATGATGGTGCGAATTTAAACGCTATTATGGACAAAGTTCGCCCAGGA
    GATATGGGATTTGATGCTGTTCATTTAAACTTGCATAAAACATTTACTGGTCCACATGGT
    GGTGGCGGTCCTGGTTCAGGTCCAGTCGGTGTAGTAAAAGAACTAGCAAGTTACTTACCA
    AAGCCAATGGTTATTAAAGATGGCGACAAATTTAAATATGATAATGACATTAAAAATTCT
    ATCGGACGTGTAAAACCATTTTATGGTAACTTTGGTATTTACTTAAGAGCTTATACGTAT
    ATTCGAACTATGGGAGCAACTGGACTTAAAGAGGTTTCTGAAGCAGCGGTTCTTAATGCG
    AATTATATTAAAGCACGTTTATCTAAACACTTTGAAATACCTTATAAACAATATTGTAAA
    CACGAGTTTGTGTTAAGTGGTGTGCGTCAAAAAGAATTTGGTGTACGTACTTTAGACATG
    GCTAAGCGATTATTAGATTTCGGTGTACATCCACCAACAATATACTTCCCATTAAATGTT
    GAAGAAGGTATGATGATTGAACCGACTGAGACAGAGTCTAAAGAAACACTTGATTATTTT
    ATCGATACATTAATTAGTATTGCTGAAGAAGCTAAAAATGATCCTGATAAAGTGCTAGAA
    GCACCACATACAACTGTGATTGATCGATTAGACGAAGCTACAGCTGCTCGTAAACCAATA
    TTAAAGTTTGAAAATCTTAAACAGGAAAAATAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    900
    960
    1020
    1080
    1140
    1200
    1260
    1320
    1380
    1440
    1473

Protein[edit source | edit]

General[edit source | edit]

  • locus tag: SACOL1593 [new locus tag: SACOL_RS08115 ]
  • symbol: SACOL1593
  • description: glycine dehydrogenase subunit 2
  • length: 490
  • theoretical pI: 5.91809
  • theoretical MW: 54780.8
  • GRAVY: -0.448571

Function[edit source | edit]

  • reaction:
    EC 1.4.4.2?  ExPASy
    Glycine dehydrogenase (aminomethyl-transferring)Glycine + [glycine-cleavage complex H protein]-N6-lipoyl-L-lysine = [glycine-cleavage complex H protein]-S-aminomethyl-N6-dihydrolipoyl-L-lysine + CO2
  • TIGRFAM:
    MetabolismEnergy metabolismAmino acids and aminesglycine dehydrogenase (TIGR00461; EC 1.4.4.2; HMM-score: 401.6)
    cysteine desulfurase, NifS family (TIGR03403; EC 2.8.1.7; HMM-score: 29)
    MetabolismBiosynthesis of cofactors, prosthetic groups, and carriersOthertyrosine decarboxylase MnfA (TIGR03812; EC 4.1.1.25; HMM-score: 26.5)
    Unknown functionEnzymes of unknown specificitycysteine desulfurase family protein (TIGR01977; HMM-score: 24.3)
    MetabolismBiosynthesis of cofactors, prosthetic groups, and carriersOthercysteine desulfurase, SufS family (TIGR01979; HMM-score: 24.2)
    Unknown functionEnzymes of unknown specificitycysteine desulfurase family protein (TIGR01976; HMM-score: 22.6)
    Genetic information processingDNA metabolismRestriction/modificationcysteine desulfurase DndA (TIGR03235; EC 2.8.1.7; HMM-score: 19.3)
    Cellular processesCellular processesBiosynthesis of natural productscapreomycidine synthase (TIGR03947; HMM-score: 17.9)
    cysteine desulfurase NifS (TIGR03402; EC 2.8.1.7; HMM-score: 17.6)
    tyrosine/nicotianamine family aminotransferase (TIGR01265; HMM-score: 13.5)
    Genetic information processingProtein synthesistRNA and rRNA base modificationcysteine desulfurase IscS (TIGR02006; EC 2.8.1.7; HMM-score: 11.6)
    MetabolismBiosynthesis of cofactors, prosthetic groups, and carriersOthercysteine desulfurase IscS (TIGR02006; EC 2.8.1.7; HMM-score: 11.6)
    MetabolismAmino acid biosynthesisHistidine familyhistidinol-phosphate transaminase (TIGR01141; EC 2.6.1.9; HMM-score: 11.1)
    MetabolismEnergy metabolismAmino acids and aminestyrosine aminotransferase (TIGR01264; EC 2.6.1.5; HMM-score: 10.5)
  • TheSEED:  
    Amino Acids and DerivativesAlanine, serine, and glycineGlycine and Serine Utilization Glycine dehydrogenase [decarboxylating] (glycine cleavage system P2 protein) (EC 1.4.4.2) 
    Alanine, serine, and glycineGlycine cleavage system Glycine dehydrogenase [decarboxylating] (glycine cleavage system P2 protein) (EC 1.4.4.2) 
    Cofactors, Vitamins, Prosthetic Groups, PigmentsLipoic acidLipoic acid metabolism Glycine dehydrogenase [decarboxylating] (glycine cleavage system P2 protein) (EC 1.4.4.2) 
  • PFAM:
    PLP_aminotran (CL0061) GDC-P; Glycine cleavage system P-protein (PF02347; HMM-score: 39)
    Aminotran_5; Aminotransferase class-V (PF00266; HMM-score: 32.4)
    Beta_elim_lyase; Beta-eliminating lyase (PF01212; HMM-score: 29.7)
    DegT_DnrJ_EryC1; DegT/DnrJ/EryC1/StrS aminotransferase family (PF01041; HMM-score: 20.7)
    Pyridoxal_deC; Pyridoxal-dependent decarboxylase conserved domain (PF00282; HMM-score: 12.4)
    Aminotran_1_2; Aminotransferase class I and II (PF00155; HMM-score: 11.2)

Structure, modifications & interactions[edit source | edit]

  • domains:
  • modifications:
  • cofactors: pyridoxal 5'-phosphate
  • effectors:
  • protein partners:

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: 0.125
    • Ymax_pos: 22
    • Cmax: 0.107
    • Cmax_pos: 37
    • Smax: 0.208
    • Smax_pos: 16
    • Smean: 0.152
    • D: 0.136
  • predicted transmembrane helices (TMHMM): 0

Accession numbers[edit source | edit]

Protein sequence[edit source | edit]

  • MTSKSSPLIFERSREGRYAYSLPKSDIKTNSVESLLDDKFIRKNKAEFPEVAELDLVRHYTELSNKNFGVDNGFYPLGSCTMKYNPKINEKVARIPGFSESHPLQDEDQVQGSLEIIYSLQEELKEITGMDEVTLQPAAGAHGEWTALMIFKAYHENNGEGHRDEVIVPDSAHGTNPASASFAGFKSVTVKSNERGEVNIDDLKRVVNENTAAIMLTNPNTLGIFEKNIMEIREIVHNAGGLLYYDGANLNAIMDKVRPGDMGFDAVHLNLHKTFTGPHGGGGPGSGPVGVVKELASYLPKPMVIKDGDKFKYDNDIKNSIGRVKPFYGNFGIYLRAYTYIRTMGATGLKEVSEAAVLNANYIKARLSKHFEIPYKQYCKHEFVLSGVRQKEFGVRTLDMAKRLLDFGVHPPTIYFPLNVEEGMMIEPTETESKETLDYFIDTLISIAEEAKNDPDKVLEAPHTTVIDRLDEATAARKPILKFENLKQEK

Experimental data[edit source | edit]

  • experimentally validated: PeptideAtlas
    experimental localization: Cytoplasmic [1] [2] [3] [4]
    quantitative data / protein copy number per cell: 157 [5]

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: 35.16 h [6]

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, 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 source | edit]