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

NCBI: 06-JUL-2013

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⊟Summary

• organism: Staphylococcus aureus Newman
locus tag: NWMN_0913 [new locus tag: NWMN_RS05115 ]
pan locus tag^?: SAUPAN003246000
symbol: memD
pan gene symbol^?: menD
• synonym:
• product: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1- carboxylic acid synthase

⊟Genome View

⊟Gene

⊟General

• type: CDS
• locus tag: NWMN_0913 [new locus tag: NWMN_RS05115 ]
• symbol: memD
• product: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1- carboxylic acid synthase
• replicon: chromosome
• strand: +
• coordinates: 1011043..1012716
• length: 1674
• essential: unknown other strains

⊟Accession numbers

• Gene ID: 5330552 NCBI
• RefSeq: YP_001331947 NCBI
• BioCyc:
• MicrobesOnline: 3706464 MicrobesOnline

⊟Phenotype

Share your knowledge and add information here. [edit]

⊟DNA sequence

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  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
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⊟Protein

⊟General

• locus tag: NWMN_0913 [new locus tag: NWMN_RS05115 ]
• symbol: MemD
• description: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1- carboxylic acid synthase
• length: 557
• theoretical pI: 6.24326
• theoretical MW: 63077.7
• GRAVY: -0.187612

⊟Function

• ⊞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
• ⊞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

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

⊟Localization

• ⊞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

• GI: 151221125 NCBI
• RefSeq: YP_001331947 NCBI
• UniProt: A6QFQ3 UniProt

⊟Protein sequence

• MGNHKAALTKQVFTFASELYAYGVREVVISPGSRSTPLALAFEAHPNIKTWIHPDERSAAFFAVGLIKGSERPVAILCTSGTAAANYTPAIAESQISRIPLIVLTSDRPHELRSVGAPQAINQVNMFNNYVSYEFDMPIADDSKETIDAIYYQMQIASQYLYGPHKGPIHFNLPFRDPLTPDLNATELLTSEMKILPHYQKSIDASALRHILNKKKGLIIVGDMQHQEVDQILTYSTIYDLPILADPLSHLRKFDHPNVICTYDLLFRSGLDLNVDFVIRVGKPVISKKLNQWLKKTDAFQILVQNNDKIDVFPIAPDISYEISANDFFRSLMEDTTVNRVSWLEKWQCLEKKGRKEIKCYLEQATDESAFVGELIKKTSEKDALFISNSMPIRDVDNLLLNKNIDVYANRGANGIDGIVSTALGMAVHKRITLLIGDLSFYHDMNGLLMSKLNNIQMNIVLLNNDGGGIFSYLPQKESATDYFERLFGTPTGLDFEYTAKLYQFDFKRFNSVSEFKNATLLSETSTIYELITNREDNFKQHQILYQKLSEMIHDTL

⊟Experimental data

• experimentally validated: data available for COL, NCTC8325
• protein localization: data available for COL
• quantitative data / protein copy number per cell: data available for COL
• interaction partners:

⊟Expression & Regulation

⊟Operon

• MicrobesOnline: NWMN_0912 > memD > NWMN_0914 > memB

⊟Regulation

• regulator:

⊟Transcription pattern

• S.aureus Expression Data Browser: data available for NCTC8325

⊟Protein synthesis (provided by Aureolib)

• Aureolib: data available for COL

⊟Protein stability

• half-life: no data available

⊞Biological Material

⊟Mutants

⊟Expression vector

⊟lacZ fusion

⊟GFP fusion

⊟two-hybrid system

⊟FLAG-tag construct

⊟Antibody

⊞Other Information

You are kindly invited to share additional interesting facts.

⊟Literature

⊟References

⊟Relevant publications