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PangenomeCOLN315NCTC8325NewmanUSA300_FPR375704-0298108BA0217611819-97685071193ECT-R 2ED133ED98HO 5096 0412JH1JH9JKD6008JKD6159JSNZLGA251M013MRSA252MSHR1132MSSA476MW2Mu3Mu50RF122ST398T0131TCH60TW20USA300_TCH1516VC40

NCBI: 03-AUG-2016

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⊟Summary[edit | edit source]

Contents

  • 1 Summary
  • 2 Genome View
  • 3 Gene
    • 3.1 General
    • 3.2 Accession numbers
    • 3.3 Phenotype
    • 3.4 DNA sequence
  • 4 Protein
    • 4.1 General
    • 4.2 Function
    • 4.3 Structure, modifications & cofactors
    • 4.4 Localization
    • 4.5 Accession numbers
    • 4.6 Protein sequence
    • 4.7 Experimental data
  • 5 Expression & Regulation
    • 5.1 Operon
    • 5.2 Regulation
    • 5.3 Transcription pattern
    • 5.4 Protein synthesis (provided by Aureolib)
    • 5.5 Protein stability
  • 6 Biological Material
    • 6.1 Mutants
    • 6.2 Expression vector
    • 6.3 lacZ fusion
    • 6.4 GFP fusion
    • 6.5 two-hybrid system
    • 6.6 FLAG-tag construct
    • 6.7 Antibody
  • 7 Other Information
  • 8 Literature
    • 8.1 References
    • 8.2 Relevant publications
  • organism: Staphylococcus aureus NCTC8325
  • locus tag: SAOUHSC_00983
  • pan locus tag?: SAUPAN003246000
  • symbol: SAOUHSC_00983
  • pan gene symbol?: menD
  • synonym:
  • product: 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylic acid synthase/2-oxoglutarate decarboxylase

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SAOUHSC_00983
  • symbol: SAOUHSC_00983
  • product: 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylic acid synthase/2-oxoglutarate decarboxylase
  • replicon: chromosome
  • strand: +
  • coordinates: 954270..955943
  • length: 1674
  • essential: no [1] DEG other strains

⊟Accession numbers[edit | edit source]

  • Gene ID: 3920128 NCBI
  • RefSeq: YP_499536 NCBI
  • BioCyc: G1I0R-926 BioCyc
  • MicrobesOnline: 1289449 MicrobesOnline

⊟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
    1441
    1501
    1561
    1621
    ATGGGAAATCATAAAGCAGCTTTAACGAAGCAAGTTTTTACATTTGCATCTGAGTTATAT
    GCGTACGGCGTAAGGGAAGTAGTTATCAGTCCGGGATCACGCTCAACGCCACTTGCACTT
    GCATTTGAAGCACATCCAAATATTAAAACATGGATACACCCCGATGAGCGAAGTGCAGCG
    TTTTTTGCAGTTGGGTTAATTAAAGGCAGTGAAAGACCTGTCGCTATATTATGTACGTCA
    GGTACAGCAGCAGCGAATTATACGCCTGCAATTGCTGAAAGCCAAATTAGTAGAATTCCT
    TTAATCGTTTTAACAAGTGACCGTCCGCATGAATTAAGAAGTGTAGGCGCACCACAAGCG
    ATTAATCAAGTAAATATGTTTAATAATTATGTAAGTTATGAGTTCGATATGCCTATTGCG
    GATGATAGTAAAGAGACCATTGATGCAATTTACTATCAAATGCAAATTGCTAGTCAATAT
    TTATATGGACCACATAAAGGGCCAATTCATTTTAACTTGCCATTTAGAGATCCGTTAACA
    CCTGATTTGAATGCAACAGAATTGTTAACTTCTGAGATGAAGATTTTACCGCACTATCAA
    AAAAGTATAGATGCATCGGCATTAAGACACATTTTAAATAAGAAAAAAGGTTTAATTATT
    GTAGGGGATATGCAGCACCAAGAAGTTGATCAAATACTAACGTATTCAACGATATATGAT
    TTGCCTATTTTAGCTGATCCTTTAAGTCATTTAAGAAAATTTGATCATCCGAATGTTATC
    TGTACATATGATTTGCTGTTTAGAAGCGGCTTAGACTTAAATGTGGATTTCGTAATTCGT
    GTTGGGAAACCAGTGATTTCTAAAAAGTTAAATCAATGGTTAAAGAAAACTGATGCATTT
    CAAATATTAGTGCAAAACAATGATAAGATTGATGTCTTTCCGATAGCGCCAGATATTTCA
    TATGAGATTTCTGCGAATGATTTCTTTAGGTCATTAATGGAAGACACGACAGTTAATCGC
    GTAAGTTGGTTAGAAAAATGGCAATGCTTAGAGAAAAAAGGGCGTAAAGAAATTAAATGT
    TATTTGGAACAAGCTACAGATGAGAGTGCATTCGTTGGTGAATTGATTAAGAAAACATCT
    GAAAAAGATGCATTATTTATTAGTAATAGTATGCCTATCAGAGATGTAGATAACTTGTTA
    TTGAATAAAAATATAGATGTCTATGCGAATCGTGGTGCGAATGGTATTGATGGTATCGTT
    TCAACTGCACTGGGTATGGCTGTGCATAAACGAATAACATTATTGATAGGTGATTTATCA
    TTTTATCATGATATGAATGGACTATTAATGTCAAAATTAAATAATATTCAGATGAATATT
    GTATTATTGAACAACGATGGTGGCGGTATTTTTTCATATTTACCACAAAAAGAAAGTGCA
    ACTGACTATTTTGAACGGTTGTTTGGCACACCGACGGGATTGGATTTCGAGTATACAGCT
    AAGTTATATCAATTCGATTTTAAACGTTTTAACAGTGTTTCAGAATTTAAAAATGCCACA
    TTGTTATCTGAAACTTCGACGATTTATGAATTGATAACGAATCGCGAAGATAACTTTAAA
    CAGCATCAAATTTTATACCAGAAATTGAGTGAAATGATTCATGACACATTATAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    900
    960
    1020
    1080
    1140
    1200
    1260
    1320
    1380
    1440
    1500
    1560
    1620
    1674

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: SAOUHSC_00983
  • symbol: SAOUHSC_00983
  • description: 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylic acid synthase/2-oxoglutarate decarboxylase
  • length: 557
  • theoretical pI: 6.24326
  • theoretical MW: 63077.7
  • GRAVY: -0.187612

⊟Function[edit | edit source]

  • ⊞reaction:
    EC 2.2.1.9?  ExPASy
    2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase Isochorismate + 2-oxoglutarate = 5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO2
    EC 4.1.1.71?  ExPASy
    2-oxoglutarate decarboxylase 2-oxoglutarate = succinate semialdehyde + CO2
  • ⊞TIGRFAM:
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Menaquinone and ubiquinone 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase (TIGR00173; EC 2.2.1.9; HMM-score: 428.2)
    and 5 more
    Metabolism Amino acid biosynthesis Pyruvate family acetolactate synthase, large subunit, biosynthetic type (TIGR00118; EC 2.2.1.6; HMM-score: 36.3)
    Metabolism Energy metabolism Sugars 3,5/4-trihydroxycyclohexa-1,2-dione hydrolase (TIGR04377; EC 3.7.1.-; HMM-score: 31.4)
    Metabolism Energy metabolism Fermentation acetolactate synthase, catabolic (TIGR02418; EC 2.2.1.6; HMM-score: 19.3)
    Metabolism Central intermediary metabolism Other sulfoacetaldehyde acetyltransferase (TIGR03457; EC 2.3.3.15; HMM-score: 16.3)
    2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase (TIGR04316; EC 1.3.1.28; HMM-score: 14.5)
  • ⊞TheSEED  :
    • 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase (EC 2.2.1.9)
    Cofactors, Vitamins, Prosthetic Groups, Pigments Quinone cofactors Menaquinone and Phylloquinone Biosynthesis  2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase (EC 2.2.1.9)
    and 1 more
    Cofactors, Vitamins, Prosthetic Groups, Pigments Quinone cofactors Menaquinone biosynthesis from chorismate via 1,4-dihydroxy-2-naphthoate  2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase (EC 2.2.1.9)
  • ⊞PFAM:
    THDP-binding (CL0254) TPP_enzyme_N; Thiamine pyrophosphate enzyme, N-terminal TPP binding domain (PF02776; HMM-score: 76.4)
    and 4 more
    NADP_Rossmann (CL0063) TPP_enzyme_M_2; Middle domain of thiamine pyrophosphate (PF16582; HMM-score: 48.5)
    THDP-binding (CL0254) TPP_enzyme_C; Thiamine pyrophosphate enzyme, C-terminal TPP binding domain (PF02775; HMM-score: 24.8)
    no clan defined ANT; Phage antirepressor protein KilAC domain (PF03374; HMM-score: 13.2)
    NADP_Rossmann (CL0063) adh_short_C2; Enoyl-(Acyl carrier protein) reductase (PF13561; HMM-score: 12.6)

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

  • domains:
  • modifications:
  • cofactors: Mg2+, Mn2+, thiamine diphosphate
  • effectors:

⊟Localization[edit | edit source]

  • ⊞PSORTb: unknown (no significant prediction)
    • Cytoplasmic Score: 2.5
    • Cytoplasmic Membrane Score: 2.5
    • Cellwall Score: 2.5
    • Extracellular Score: 2.5
    • Internal Helices: 0
  • ⊞DeepLocPro: Cytoplasmic
    • Cytoplasmic Score: 0.9722
    • Cytoplasmic Membrane Score: 0.0171
    • Cell wall & surface Score: 0.0029
    • Extracellular Score: 0.0078
  • ⊞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): 0.034937
    • TAT(Tat/SPI): 0.007695
    • LIPO(Sec/SPII): 0.004206
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

  • GI: 88194740 NCBI
  • RefSeq: YP_499536 NCBI
  • UniProt: Q2FZL7 UniProt
  • STRING: 93061.SAOUHSC_00983 STRING

⊟Protein sequence[edit | edit source]

  • MGNHKAALTKQVFTFASELYAYGVREVVISPGSRSTPLALAFEAHPNIKTWIHPDERSAAFFAVGLIKGSERPVAILCTSGTAAANYTPAIAESQISRIPLIVLTSDRPHELRSVGAPQAINQVNMFNNYVSYEFDMPIADDSKETIDAIYYQMQIASQYLYGPHKGPIHFNLPFRDPLTPDLNATELLTSEMKILPHYQKSIDASALRHILNKKKGLIIVGDMQHQEVDQILTYSTIYDLPILADPLSHLRKFDHPNVICTYDLLFRSGLDLNVDFVIRVGKPVISKKLNQWLKKTDAFQILVQNNDKIDVFPIAPDISYEISANDFFRSLMEDTTVNRVSWLEKWQCLEKKGRKEIKCYLEQATDESAFVGELIKKTSEKDALFISNSMPIRDVDNLLLNKNIDVYANRGANGIDGIVSTALGMAVHKRITLLIGDLSFYHDMNGLLMSKLNNIQMNIVLLNNDGGGIFSYLPQKESATDYFERLFGTPTGLDFEYTAKLYQFDFKRFNSVSEFKNATLLSETSTIYELITNREDNFKQHQILYQKLSEMIHDTL

⊟Experimental data[edit | edit source]

  • experimentally validated: PeptideAtlas [2] [3]
  • protein localization: data available for COL
  • quantitative data / protein copy number per cell: data available for COL
  • interaction partners:

⊟Expression & Regulation[edit | edit source]

⊟Operon[edit | edit source]

  • MicrobesOnline: SAOUHSC_00982 > SAOUHSC_00983 > SAOUHSC_00984 > SAOUHSC_00985
    predicted SigA promoter [4] : S404 > SAOUHSC_00981 > S405 > SAOUHSC_00982 > SAOUHSC_00983 > SAOUHSC_00984 > SAOUHSC_00985
    predicted SigA promoter [4] : SAOUHSC_00981 > S405 > SAOUHSC_00982 > SAOUHSC_00983 > SAOUHSC_00984 > SAOUHSC_00985

⊟Regulation[edit | edit source]

  • regulator:

⊟Transcription pattern[edit | edit source]

  • S.aureus Expression Data Browser:  [4] 
    Expression Data Browser
    ⊟Multi-gene expression profiles

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

  • Aureolib: data available for COL

⊟Protein stability[edit | edit source]

  • half-life: no data available

⊞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. ↑ Roy R Chaudhuri, Andrew G Allen, Paul J Owen, Gil Shalom, Karl Stone, Marcus Harrison, Timothy A Burgis, Michael Lockyer, Jorge Garcia-Lara, Simon J Foster, Stephen J Pleasance, Sarah E Peters, Duncan J Maskell, Ian G Charles
    Comprehensive identification of essential Staphylococcus aureus genes using Transposon-Mediated Differential Hybridisation (TMDH).
    BMC Genomics: 2009, 10;291
    [PubMed:19570206] [WorldCat.org] [DOI] (I e)
  2. ↑ Maren Depke, Stephan Michalik, Alexander Rabe, Kristin Surmann, Lars Brinkmann, Nico Jehmlich, Jörg Bernhardt, Michael Hecker, Bernd Wollscheid, Zhi Sun, Robert L Moritz, Uwe Völker, Frank Schmidt
    A peptide resource for the analysis of Staphylococcus aureus in host-pathogen interaction studies.
    Proteomics: 2015, 15(21);3648-61
    [PubMed:26224020] [WorldCat.org] [DOI] (I p)
  3. ↑ Stephan Michalik, Maren Depke, Annette Murr, Manuela Gesell Salazar, Ulrike Kusebauch, Zhi Sun, Tanja C Meyer, Kristin Surmann, Henrike Pförtner, Petra Hildebrandt, Stefan Weiss, Laura Marcela Palma Medina, Melanie Gutjahr, Elke Hammer, Dörte Becher, Thomas Pribyl, Sven Hammerschmidt, Eric W Deutsch, Samuel L Bader, Michael Hecker, Robert L Moritz, Ulrike Mäder, Uwe Völker, Frank Schmidt
    A global Staphylococcus aureus proteome resource applied to the in vivo characterization of host-pathogen interactions.
    Sci Rep: 2017, 7(1);9718
    [PubMed:28887440] [WorldCat.org] [DOI] (I e)
  4. ↑ Jump up to: 4.0 4.1 4.2 Ulrike Mäder, Pierre Nicolas, Maren Depke, Jan Pané-Farré, Michel Debarbouille, Magdalena M van der Kooi-Pol, Cyprien Guérin, Sandra Dérozier, Aurelia Hiron, Hanne Jarmer, Aurélie Leduc, Stephan Michalik, Ewoud Reilman, Marc Schaffer, Frank Schmidt, Philippe Bessières, Philippe Noirot, Michael Hecker, Tarek Msadek, Uwe Völker, Jan Maarten van Dijl
    Staphylococcus aureus Transcriptome Architecture: From Laboratory to Infection-Mimicking Conditions.
    PLoS Genet: 2016, 12(4);e1005962
    [PubMed:27035918] [WorldCat.org] [DOI] (I e)

⊟Relevant publications[edit | edit source]

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  • This page was last edited on 11 March 2016, at 11:07.
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