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NCBI: 06-JUL-2013

Summary[edit | edit source]

  • organism: Staphylococcus aureus Newman
  • locus tag: NWMN_0942 [new locus tag: NWMN_RS05275 ]
  • 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: NWMN_0942 [new locus tag: NWMN_RS05275 ]
  • symbol: purD
  • product: phosphoribosylamine--glycine ligase
  • replicon: chromosome
  • strand: +
  • coordinates: 1046082..1047329
  • length: 1248
  • 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
    ATGAATGTATTAGTAATTGGTGCTGGTGGACGAGAACATGCACTTGCATATAAACTTAAT
    CAATCGAATCTAGTTAAACAAGTGTTTGTCATTCCAGGTAATGAGGCAATGACACCTATA
    GCTGAAGTACACACTGAAATTTCAGAACCTGATCATCAAGCGATACTAGATTTTGCTAAA
    CGGCAAAATGTTGATTGGGTAGTTATAGGTCCAGAACAGCCGCTAATTGATGGATTAGCA
    GACATTTTACGAGCGAATGGTTTCAAAGTGTTTGGTCCAAATAAGCAAGCAGCTCAAATC
    GAAGGCTCAAAATTATTTGCTAAAAAGATAATGGAAAAATATAATATTCCAACTGCTGAT
    TATAAAGAAGTTGAGCGAAAAAAGGATGCTTTAACATATATTGAAAACTGTGAATTGCCC
    GTTGTTGTCAAGAAAGATGGGTTAGCTGCTGGGAAAGGCGTTATTATTGCAGATACTATT
    GAAGCAGCCAGAAGTGCTATTGAGATTATGTATGGTGATGAAGAAGAAGGTACTGTTGTA
    TTTGAAACGTTTTTAGAAGGTGAAGAGTTCTCGCTAATGACATTTGTTAATGGTGATTTA
    GCAGTACCTTTCGACTGTATTGCACAAGATCATAAACGCGCATTTGATCATGATGAAGGA
    CCAAATACTGGTGGTATGGGGGCTTATTGTCCAGTACCACATATTAGTGACGATGTTTTA
    AAACTTACAAATGAAACAATTGCACAACCCATTGCAAAGGCAATGCTTAATGAAGGTTAT
    CAATTCTTCGGTGTATTATACATTGGTGCTATTTTAACTAAAGATGGTCCAAAAGTAATA
    GAATTTAATGCCCGTTTTGGTGATCCTGAAGCTCAAGTATTATTAAGTCGCATGGAAAGT
    GATTTAATGCAGCATATTATTGATTTAGATGAAGGAAAACGTACTGAATTCAAATGGAAA
    AATGAATCTATTGTAGGGGTCATGTTGGCATCAAAAGGATATCCTGATGCATATGAAAAA
    GGGCATAAAGTAAGTGGCTTTGATTTAAATGAAAACTATTTTGTTAGTGGATTAAAGAAG
    CAAGGTGATACCTTTGTTACTTCAGGTGGTAGAGTTATACTTGCCATCGGAAAAGGTGAC
    AATGTACAAGATGCACAGCGAGACGCATACAAAAAAGTATCACAAATACAAAGTGACCAT
    TTATTCTATCGTCATGACATTGCGAATAAAGCACTACAACTTAAATAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    900
    960
    1020
    1080
    1140
    1200
    1248

Protein[edit | edit source]

General[edit | edit source]

  • locus tag: NWMN_0942 [new locus tag: NWMN_RS05275 ]
  • symbol: PurD
  • description: phosphoribosylamine--glycine ligase
  • length: 415
  • theoretical pI: 4.89379
  • theoretical MW: 45858.9
  • GRAVY: -0.244819

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: 466)
    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: 36.2)
    Metabolism Purines, pyrimidines, nucleosides, and nucleotides Purine ribonucleotide biosynthesis phosphoribosylaminoimidazole carboxylase, ATPase subunit (TIGR01161; EC 4.1.1.21; HMM-score: 29.2)
    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: 28.3)
    Cellular processes Cellular processes Biosynthesis of natural products cyanophycin synthetase (TIGR02068; EC 6.3.2.29,6.3.2.30; HMM-score: 24.7)
    Metabolism Fatty acid and phospholipid metabolism Biosynthesis acetyl-CoA carboxylase, biotin carboxylase subunit (TIGR00514; EC 6.3.4.14; HMM-score: 22.4)
    alpha-L-glutamate ligase, RimK family (TIGR00768; EC 6.3.2.-; HMM-score: 22.2)
    Metabolism Purines, pyrimidines, nucleosides, and nucleotides Purine ribonucleotide biosynthesis phosphoribosylglycinamide formyltransferase 2 (TIGR01142; EC 2.1.2.-; HMM-score: 19.4)
    Metabolism Energy metabolism TCA cycle succinate-CoA ligase, beta subunit (TIGR01016; EC 6.2.1.-; HMM-score: 14.6)
    Metabolism Energy metabolism Glycolysis/gluconeogenesis pyruvate carboxylase (TIGR01235; EC 6.4.1.1; HMM-score: 14.2)
    Metabolism Amino acid biosynthesis Other pyrrolysine biosynthesis protein PylC (TIGR03909; HMM-score: 13.7)
    lysine biosynthesis enzyme LysX (TIGR02144; HMM-score: 13.1)
  • TheSEED: data available for COL, N315, NCTC8325, USA300_FPR3757
  • PFAM:
    ATP-grasp (CL0179) GARS_A; Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain (PF01071; HMM-score: 225.8)
    and 9 more
    PreATP-grasp (CL0483) GARS_N; Phosphoribosylglycinamide synthetase, N domain (PF02844; HMM-score: 118)
    Hybrid (CL0105) GARS_C; Phosphoribosylglycinamide synthetase, C domain (PF02843; HMM-score: 84.1)
    ATP-grasp (CL0179) ATP-grasp_3; ATP-grasp domain (PF02655; HMM-score: 29.6)
    ATP-grasp; ATP-grasp domain (PF02222; HMM-score: 23.1)
    ATPgrasp_Ter; ATP-grasp in the biosynthetic pathway with Ter operon (PF15632; HMM-score: 17.7)
    RimK; RimK-like ATP-grasp domain (PF08443; HMM-score: 17.2)
    CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain (PF02786; HMM-score: 15.8)
    ATP-grasp_5; ATP-grasp domain (PF13549; HMM-score: 14.4)
    ATP-grasp_2; ATP-grasp domain (PF08442; HMM-score: 13)

Structure, modifications & cofactors[edit | edit source]

  • domains:
  • modifications:
  • cofactors:
  • 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
  • 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): 0.008564
    • TAT(Tat/SPI): 0.000596
    • LIPO(Sec/SPII): 0.001631
  • predicted transmembrane helices (TMHMM): 0

Accession numbers[edit | edit source]

Protein sequence[edit | edit source]

  • MNVLVIGAGGREHALAYKLNQSNLVKQVFVIPGNEAMTPIAEVHTEISEPDHQAILDFAKRQNVDWVVIGPEQPLIDGLADILRANGFKVFGPNKQAAQIEGSKLFAKKIMEKYNIPTADYKEVERKKDALTYIENCELPVVVKKDGLAAGKGVIIADTIEAARSAIEIMYGDEEEGTVVFETFLEGEEFSLMTFVNGDLAVPFDCIAQDHKRAFDHDEGPNTGGMGAYCPVPHISDDVLKLTNETIAQPIAKAMLNEGYQFFGVLYIGAILTKDGPKVIEFNARFGDPEAQVLLSRMESDLMQHIIDLDEGKRTEFKWKNESIVGVMLASKGYPDAYEKGHKVSGFDLNENYFVSGLKKQGDTFVTSGGRVILAIGKGDNVQDAQRDAYKKVSQIQSDHLFYRHDIANKALQLK

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:
    NWMN_1483(dnaK)molecular chaperone DnaK  [1] (data from MRSA252)
    NWMN_0961(pdhC)branched-chain alpha-keto acid dehydrogenase subunit E2  [1] (data from MRSA252)
    NWMN_0962(pdhD)dihydrolipoamide dehydrogenase  [1] (data from MRSA252)
    NWMN_0959(phdA)pyruvate dehydrogenase E1 component, alpha subunit  [1] (data from MRSA252)
    NWMN_0960(phdB)pyruvate dehydrogenase E1 component, beta subunit  [1] (data from MRSA252)
    NWMN_1592(pykA)pyruvate kinase  [1] (data from MRSA252)
    NWMN_0500(rplA)50S ribosomal protein L1  [1] (data from MRSA252)
    NWMN_2149(rplB)50S ribosomal protein L2  [1] (data from MRSA252)
    NWMN_2137(rplF)50S ribosomal protein L6  [1] (data from MRSA252)
    NWMN_0501(rplJ)50S ribosomal protein L10  [1] (data from MRSA252)
    NWMN_2133(rplO)50S ribosomal protein L15  [1] (data from MRSA252)
    NWMN_1151(rplS)50S ribosomal protein L19  [1] (data from MRSA252)
    NWMN_1549(rplU)50S ribosomal protein L21  [1] (data from MRSA252)
    NWMN_2150(rplW)50S ribosomal protein L23  [1] (data from MRSA252)
    NWMN_1613(rpsD)30S ribosomal protein S4  [1] (data from MRSA252)
    NWMN_2135(rpsE)30S ribosomal protein S5  [1] (data from MRSA252)
    NWMN_2119(rpsI)30S ribosomal protein S9  [1] (data from MRSA252)
    NWMN_2127(rpsK)30S ribosomal protein S11  [1] (data from MRSA252)
    NWMN_0510(tufA)elongation factor Tu  [1] (data from MRSA252)
    NWMN_1382DNA-binding protein HU  [1] (data from MRSA252)
    NWMN_1600universal stress protein family protein  [1] (data from MRSA252)
    NWMN_2086alkaline shock protein 23  [1] (data from MRSA252)

Expression & Regulation[edit | edit source]

Regulation[edit | edit source]

  • data available for N315

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. 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]