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NCBI: 10-JUN-2013

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus COL
  • locus tag: SACOL2105 [new locus tag: SACOL_RS11015 ]
  • pan locus tag?: SAUPAN005404000
  • symbol: glyA
  • pan gene symbol?: glyA
  • synonym:
  • product: serine hydroxymethyltransferase

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SACOL2105 [new locus tag: SACOL_RS11015 ]
  • symbol: glyA
  • product: serine hydroxymethyltransferase
  • replicon: chromosome
  • strand: -
  • coordinates: 2165590..2166828
  • length: 1239
  • 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
    ATGTCTTATATCACCAAGCAAGATAAAGTTATCGCAGAAGCAATCGAGAGAGAATTTCAG
    AGACAAAATAGCAACATAGAGTTAATCGCATCGGAAAATTTTGTATCGGAAGCGGTTATG
    GAAGCACAAGGTTCAGTGTTGACTAATAAGTATGCTGAAGGCTATCCAGGACGCCGATAT
    TATGGTGGCTGTGAGTTTGTAGATGTTACTGAAAGCATCGCAATTGATCGTGCTAAAGCA
    TTGTTTGGAGCTGAACATGTCAATGTTCAACCACATTCAGGTTCACAAGCGAACATGGCT
    GTTTACTTAGTTGCATTAGAAATGGGCGACACAGTTTTAGGTATGAATTTGAGTCATGGT
    GGTCACTTGACACATGGAGCGCCTGTTAATTTTAGTGGTAAATTCTACAATTTCGTTGAA
    TATGGAGTAGATAAAGACACAGAACGAATCAATTATGATGAAGTTCGTAAATTAGCGTTA
    GAGCATAAGCCTAAGCTTATTGTGGCAGGAGCATCAGCATATTCAAGAACAATTGACTTC
    AAAAAGTTTAAAGAAATCGCAGATGAAGTAAACGCTAAGTTAATGGTAGACATGGCACAT
    ATTGCAGGATTAGTAGCGGCAGGTTTACATCCAAATCCAGTAGAATATGCTGATTTTGTA
    ACAACTACAACACACAAAACATTACGCGGACCACGTGGTGGTATGATTTTATGTAAGGAA
    GAATATAAAAAAGACATAGATAAAACAATTTTCCCTGGTATTCAAGGTGGACCTCTTGAG
    CATGTTATTGCAGCAAAAGCAGTTGCTTTTGGAGAAGCGTTAGAAAATAATTTCAAAACG
    TATCAACAACAAGTGGTTAAAAACGCAAAAGTTCTTGCAGAAGCATTAATTAATGAAGGA
    TTTAGAATTGTTTCTGGCGGTACAGATAATCACTTAGTAGCTGTTGATGTAAAAGGGTCT
    ATAGGACTTACTGGTAAAGAAGCTGAAGAGACTTTAGATTCAGTTGGTATCACATGTAAC
    AAAAATACCATTCCGTTCGATCAAGAAAAACCTTTTGTAACGAGTGGTATACGTTTAGGT
    ACACCTGCTGCAACAACGCGTGGATTTGATGAAAAAGCTTTTGAGGAAGTTGCAAAAATC
    ATCAGTTTAGCATTGAAAAATAGTAAAGATGAAGAAAAATTACAACAAGCTAAAGAACGC
    GTTGCGAAATTAACAGCTGAATATCCTCTATATCAATAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    900
    960
    1020
    1080
    1140
    1200
    1239

⊟Protein[edit | edit source]

Protein Data Bank: 3PGY

⊟General[edit | edit source]

  • locus tag: SACOL2105 [new locus tag: SACOL_RS11015 ]
  • symbol: GlyA
  • description: serine hydroxymethyltransferase
  • length: 412
  • theoretical pI: 5.99288
  • theoretical MW: 45172
  • GRAVY: -0.269417

⊟Function[edit | edit source]

  • ⊞reaction:
    EC 2.1.2.1?  ExPASy
    Glycine hydroxymethyltransferase 5,10-methylenetetrahydrofolate + glycine + H2O = tetrahydrofolate + L-serine
  • ⊞TIGRFAM:
    Cellular processes Cellular processes Biosynthesis of natural products fluorothreonine transaldolase (TIGR04506; EC 2.2.1.8; HMM-score: 114.6)
    and 7 more
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Biotin 8-amino-7-oxononanoate synthase (TIGR00858; EC 2.3.1.47; HMM-score: 26.8)
    Unknown function Enzymes of unknown specificity cysteine desulfurase family protein (TIGR01977; HMM-score: 22.3)
    Unknown function Enzymes of unknown specificity pyridoxal phosphate enzyme, MJ0158 family (TIGR03576; HMM-score: 20)
    Metabolism Energy metabolism Amino acids and amines glycine C-acetyltransferase (TIGR01822; EC 2.3.1.29; HMM-score: 18.8)
    UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine transaminase (TIGR03588; EC 2.6.1.92; HMM-score: 16.6)
    dTDP-4-dehydro-6-deoxyglucose aminotransferase (TIGR04427; EC 2.-.-.-; HMM-score: 14.1)
    putative methanogenesis marker protein 8 (TIGR03275; HMM-score: 12.8)
  • ⊞TheSEED  :
    • Serine hydroxymethyltransferase (EC 2.1.2.1)
    Amino Acids and Derivatives Alanine, serine, and glycine Glycine and Serine Utilization  Serine hydroxymethyltransferase (EC 2.1.2.1)
    and 6 more
    Amino Acids and Derivatives Alanine, serine, and glycine Glycine Biosynthesis  Serine hydroxymethyltransferase (EC 2.1.2.1)
    Amino Acids and Derivatives Alanine, serine, and glycine Glycine cleavage system  Serine hydroxymethyltransferase (EC 2.1.2.1)
    Amino Acids and Derivatives Alanine, serine, and glycine Serine Biosynthesis  Serine hydroxymethyltransferase (EC 2.1.2.1)
    Carbohydrates One-carbon Metabolism Serine-glyoxylate cycle  Serine hydroxymethyltransferase (EC 2.1.2.1)
    Cofactors, Vitamins, Prosthetic Groups, Pigments Folate and pterines Folate Biosynthesis  Serine hydroxymethyltransferase (EC 2.1.2.1)
    Stress Response Stress Response - no subcategory Flavohaemoglobin  Serine hydroxymethyltransferase (EC 2.1.2.1)
  • ⊞PFAM:
    PLP_aminotran (CL0061) SHMT; Serine hydroxymethyltransferase (PF00464; HMM-score: 589.1)
    and 5 more
    Beta_elim_lyase; Beta-eliminating lyase (PF01212; HMM-score: 29.9)
    Aminotran_1_2; Aminotransferase class I and II (PF00155; HMM-score: 28)
    DegT_DnrJ_EryC1; DegT/DnrJ/EryC1/StrS aminotransferase family (PF01041; HMM-score: 13.4)
    Aminotran_5; Aminotransferase class-V (PF00266; HMM-score: 13.1)
    Cys_Met_Meta_PP; Cys/Met metabolism PLP-dependent enzyme (PF01053; HMM-score: 11.5)

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

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

⊟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
  • ⊞DeepLocPro: Cytoplasmic
    • Cytoplasmic Score: 0.8918
    • Cytoplasmic Membrane Score: 0.0012
    • Cell wall & surface Score: 0.0001
    • Extracellular Score: 0.1069
  • ⊞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): 0.005746
    • TAT(Tat/SPI): 0.001573
    • LIPO(Sec/SPII): 0.000815
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MSYITKQDKVIAEAIEREFQRQNSNIELIASENFVSEAVMEAQGSVLTNKYAEGYPGRRYYGGCEFVDVTESIAIDRAKALFGAEHVNVQPHSGSQANMAVYLVALEMGDTVLGMNLSHGGHLTHGAPVNFSGKFYNFVEYGVDKDTERINYDEVRKLALEHKPKLIVAGASAYSRTIDFKKFKEIADEVNAKLMVDMAHIAGLVAAGLHPNPVEYADFVTTTTHKTLRGPRGGMILCKEEYKKDIDKTIFPGIQGGPLEHVIAAKAVAFGEALENNFKTYQQQVVKNAKVLAEALINEGFRIVSGGTDNHLVAVDVKGSIGLTGKEAEETLDSVGITCNKNTIPFDQEKPFVTSGIRLGTPAATTRGFDEKAFEEVAKIISLALKNSKDEEKLQQAKERVAKLTAEYPLYQ

⊟Experimental data[edit | edit source]

  • experimentally validated: PeptideAtlas
  • protein localization: Cytoplasmic [1] [2] [3] [4]
  • quantitative data / protein copy number per cell: 2758 [5]
  • ⊟interaction partners:
    SACOL1102(pdhA)pyruvate dehydrogenase complex E1 component subunit alpha  [6] (data from MRSA252)
    SACOL2227(rplE)50S ribosomal protein L5  [6] (data from MRSA252)
    SACOL2222(rpsE)30S ribosomal protein S5  [6] (data from MRSA252)
    SACOL0594(tuf)elongation factor Tu  [6] (data from MRSA252)
    SACOL2104(upp)uracil phosphoribosyltransferase  [6] (data from MRSA252)
    SACOL0211acetyl-CoA acetyltransferase  [6] (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: 19.22 h [7]

⊞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. ↑ Jump up to: 6.0 6.1 6.2 6.3 6.4 6.5 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)
  7. ↑ 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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