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NCBI: 26-AUG-2013

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus N315
  • locus tag: SA0926 [new locus tag: SA_RS05245 ]
  • pan locus tag?: SAUPAN003287000
  • symbol: purD
  • pan gene symbol?: purD
  • synonym:
  • product: phosphoribosylamine--glycine ligase

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SA0926 [new locus tag: SA_RS05245 ]
  • symbol: purD
  • product: phosphoribosylamine--glycine ligase
  • replicon: chromosome
  • strand: +
  • coordinates: 1051699..1052838
  • length: 1140
  • essential: no DEG 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
    ATGACACCTATAGCTGAAGTACACACTGAAATTTCAGAATCTAATCATCAAGGGATACTA
    GATTTTGCTAAACAGCAAAATGTTGATTGGGTAGTTATAGGTCCAGAACAGCCGCTAATT
    GATGGATTAGCAGACATTTTACGAGCGAATGGTTTCAAAGTGTTTGGTCCAAATAAGCAA
    GCAGCTCAAATCGAAGGCTCAAAATTATTTGCTAAAAAGATAATGAAAAAATATAATATT
    CCAACTGCTGATTATAAAGAAGTTGAGCGAAAAAAGGATGCTTTAACATATATTGAAAAC
    TGTGAATTGCCCGTTGTTGTCAAGAAAGATGGGTTAGCTGCTGGGAAAGGCGTTATTATT
    GCAGATACTATTGAAGCAGCCAGAAGTGCTATTGAGATTATGTATGGTGATGAAGAAGAA
    GGTACTGTTGTATTTGAAACGTTTTTAGAAGGTGAAGAGTTCTCGCTAATGACATTTGTT
    AATGGTGATTTAGCAGTACCTTTCGACTGTATTGCACAAGATCATAAACGCGCATTTGAT
    CATGATGAAGGACCAAATACTGGTGGTATGGGGGCTTATTGTCCAGTACCACATATTAGT
    GACGATGTTTTAAAACTTACAAATGAAACAATTGCACAACCCATTGCAAAGGCAATGCTT
    AATGAAGGTTATCAATTCTTCGGTGTATTATACATTGGTGCTATTTTAACTAAAGATGGT
    CCAAAAGTAATAGAATTTAATGCCCGTTTTGGTGATCCTGAAGCTCAAGTATTATTAAGT
    CGCATGGAAAGTGATTTAATGCAGCATATTATTGATTTAGATGAAGGAAAACGTACTGAA
    TTCAAATGGAAAAATGAATCTATTGTAGGGGTCATGTTGGCATCAAAAGGATATCCTGAT
    GCATATGAAAAAGGGCATAAAGTAAGTGGCTTTGATTTAAATGAAAACTATTTTGTTAGT
    GGATTAAAGAAGCAAGGTGATACCTTTGTTACTTCAGGTGGTAGAGTTATACTTGCCATC
    GGAAAAGGTGACAATGTACAAGATGCACAGCGAGACGCATACGAAAAAGTATCTCAAATA
    CAAAGTGACCATTTATTCTATCGTCATGACATTGCGAATAAAGCACTACAACTTAAATAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    900
    960
    1020
    1080
    1140

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: SA0926 [new locus tag: SA_RS05245 ]
  • symbol: PurD
  • description: phosphoribosylamine--glycine ligase
  • length: 379
  • theoretical pI: 4.74913
  • theoretical MW: 41972.3
  • GRAVY: -0.291029

⊟Function[edit | edit source]

  • ⊞reaction:
    EC 6.3.4.13?  ExPASy
    Phosphoribosylamine--glycine ligase ATP + 5-phospho-D-ribosylamine + glycine = ADP + phosphate + N1-(5-phospho-D-ribosyl)glycinamide
  • ⊞TIGRFAM:
    Metabolism Purines, pyrimidines, nucleosides, and nucleotides Purine ribonucleotide biosynthesis phosphoribosylamine--glycine ligase (TIGR00877; EC 6.3.4.13; HMM-score: 417.3)
    and 11 more
    Metabolism Purines, pyrimidines, nucleosides, and nucleotides Pyrimidine ribonucleotide biosynthesis carbamoyl-phosphate synthase, large subunit (TIGR01369; EC 6.3.5.5; HMM-score: 36)
    Cell structure Cell envelope Biosynthesis and degradation of murein sacculus and peptidoglycan D-alanine--D-alanine ligase (TIGR01205; EC 6.3.2.4; HMM-score: 29.2)
    Metabolism Purines, pyrimidines, nucleosides, and nucleotides Purine ribonucleotide biosynthesis phosphoribosylaminoimidazole carboxylase, ATPase subunit (TIGR01161; EC 4.1.1.21; HMM-score: 26.2)
    Cellular processes Cellular processes Biosynthesis of natural products cyanophycin synthetase (TIGR02068; EC 6.3.2.29,6.3.2.30; HMM-score: 25.2)
    Metabolism Fatty acid and phospholipid metabolism Biosynthesis acetyl-CoA carboxylase, biotin carboxylase subunit (TIGR00514; EC 6.3.4.14; HMM-score: 24.7)
    alpha-L-glutamate ligase, RimK family (TIGR00768; EC 6.3.2.-; HMM-score: 22)
    Metabolism Energy metabolism TCA cycle succinate-CoA ligase, beta subunit (TIGR01016; EC 6.2.1.-; HMM-score: 15.1)
    Metabolism Purines, pyrimidines, nucleosides, and nucleotides Purine ribonucleotide biosynthesis phosphoribosylglycinamide formyltransferase 2 (TIGR01142; EC 2.1.2.-; HMM-score: 14.6)
    Metabolism Amino acid biosynthesis Other pyrrolysine biosynthesis protein PylC (TIGR03909; HMM-score: 14.1)
    Metabolism Energy metabolism Glycolysis/gluconeogenesis pyruvate carboxylase (TIGR01235; EC 6.4.1.1; HMM-score: 13.9)
    lysine biosynthesis enzyme LysX (TIGR02144; HMM-score: 13.9)
  • ⊞TheSEED  :
    • Phosphoribosylamine--glycine ligase (EC 6.3.4.13)
    Miscellaneous Miscellaneous - no subcategory EC 6.3.4.- Ligases that form carbon-nitrogen bonds  Phosphoribosylamine--glycine ligase (EC 6.3.4.13)
    and 1 more
    Nucleosides and Nucleotides Purines De Novo Purine Biosynthesis  Phosphoribosylamine--glycine ligase (EC 6.3.4.13)
  • ⊞PFAM:
    ATP-grasp (CL0179) GARS_A; Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain (PF01071; HMM-score: 229.3)
    and 10 more
    Hybrid (CL0105) GARS_C; Phosphoribosylglycinamide synthetase, C domain (PF02843; HMM-score: 86.8)
    NADP_Rossmann (CL0063) GARS_N; Phosphoribosylglycinamide synthetase, N domain (PF02844; HMM-score: 64.5)
    ATP-grasp (CL0179) ATP-grasp_3; ATP-grasp domain (PF02655; HMM-score: 30)
    ATP-grasp; ATP-grasp domain (PF02222; HMM-score: 25.1)
    RimK; RimK-like ATP-grasp domain (PF08443; HMM-score: 18.1)
    Dala_Dala_lig_C; D-ala D-ala ligase C-terminus (PF07478; HMM-score: 17.5)
    CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain (PF02786; HMM-score: 16.8)
    ATP-grasp_5; ATP-grasp domain (PF13549; HMM-score: 16.5)
    MurF-HprK_N (CL0365) Mur_ligase; Mur ligase family, catalytic domain (PF01225; HMM-score: 16.4)
    ATP-grasp (CL0179) ATP-grasp_2; ATP-grasp domain (PF08442; HMM-score: 14.2)

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

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

⊟Localization[edit | edit source]

  • ⊞PSORTb: Cytoplasmic
    • Cytoplasmic Score: 7.5
    • Cytoplasmic Membrane Score: 1.15
    • Cellwall Score: 0.62
    • Extracellular Score: 0.73
    • Internal Helices: 0
  • ⊞DeepLocPro: Cytoplasmic
    • Cytoplasmic Score: 0.9787
    • Cytoplasmic Membrane Score: 0.0011
    • Cell wall & surface Score: 0.0005
    • Extracellular Score: 0.0197
  • ⊞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): 0.002388
    • TAT(Tat/SPI): 0.000206
    • LIPO(Sec/SPII): 0.000296
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MTPIAEVHTEISESNHQGILDFAKQQNVDWVVIGPEQPLIDGLADILRANGFKVFGPNKQAAQIEGSKLFAKKIMKKYNIPTADYKEVERKKDALTYIENCELPVVVKKDGLAAGKGVIIADTIEAARSAIEIMYGDEEEGTVVFETFLEGEEFSLMTFVNGDLAVPFDCIAQDHKRAFDHDEGPNTGGMGAYCPVPHISDDVLKLTNETIAQPIAKAMLNEGYQFFGVLYIGAILTKDGPKVIEFNARFGDPEAQVLLSRMESDLMQHIIDLDEGKRTEFKWKNESIVGVMLASKGYPDAYEKGHKVSGFDLNENYFVSGLKKQGDTFVTSGGRVILAIGKGDNVQDAQRDAYEKVSQIQSDHLFYRHDIANKALQLK

⊟Experimental data[edit | edit source]

  • 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:
    SA1984(asp23)alkaline shock protein 23  [1] (data from MRSA252)
    SA1409(dnaK)molecular chaperone DnaK  [1] (data from MRSA252)
    SA1305(hu)DNA-binding protein II  [1] (data from MRSA252)
    SA0943-1(pdhA)pyruvate dehydrogenase E1 component subunit alpha  [1] (data from MRSA252)
    SA0944(pdhB)pyruvate dehydrogenase E1 component subunit beta  [1] (data from MRSA252)
    SA0945(pdhC)branched-chain alpha-keto acid dehydrogenase E2 subunit  [1] (data from MRSA252)
    SA0946(pdhD)dihydrolipoamide dehydrogenase  [1] (data from MRSA252)
    SA1520(pykA)pyruvate kinase  [1] (data from MRSA252)
    SA0496(rplA)50S ribosomal protein L1  [1] (data from MRSA252)
    SA2044(rplB)50S ribosomal protein L2  [1] (data from MRSA252)
    SA2033(rplF)50S ribosomal protein L6  [1] (data from MRSA252)
    SA0497(rplJ)50S ribosomal protein L10  [1] (data from MRSA252)
    SA2029(rplO)50S ribosomal protein L15  [1] (data from MRSA252)
    SA1084(rplS)50S ribosomal protein L19  [1] (data from MRSA252)
    SA1473(rplU)50S ribosomal protein L21  [1] (data from MRSA252)
    SA2045(rplW)50S ribosomal protein L23  [1] (data from MRSA252)
    SAS052(rpsD)30S ribosomal protein S4  [1] (data from MRSA252)
    SA2031(rpsE)30S ribosomal protein S5  [1] (data from MRSA252)
    SA2016(rpsI)30S ribosomal protein S9  [1] (data from MRSA252)
    SA2024(rpsK)30S ribosomal protein S11  [1] (data from MRSA252)
    SA0506(tuf)elongation factor Tu  [1] (data from MRSA252)
    SA1528hypothetical protein  [1] (data from MRSA252)

⊟Expression & Regulation[edit | edit source]

⊟Operon[edit | edit source]

⊟Regulation[edit | edit source]

  • ⊞regulator: PurR (repression) regulon

⊟Transcription pattern[edit | edit source]

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

⊟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. ↑ Jump up to: 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 1.14 1.15 1.16 1.17 1.18 1.19 1.20 1.21 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)

⊟Relevant publications[edit | edit source]

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