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NCBI: 10-JUN-2013

Summary[edit source | edit]

  • organism: Staphylococcus aureus COL
  • locus tag: SACOL1083 [new locus tag: SACOL_RS05525 ]
  • pan locus tag?: SAUPAN003287000
  • symbol: purD
  • pan gene symbol?: purD
  • synonym:
  • product: phosphoribosylamine--glycine ligase

Genome View[edit source | edit]

Gene[edit source | edit]

General[edit source | edit]

  • type: CDS
  • locus tag: SACOL1083 [new locus tag: SACOL_RS05525 ]
  • symbol: purD
  • product: phosphoribosylamine--glycine ligase
  • replicon: chromosome
  • strand: +
  • coordinates: 1092909..1094156
  • length: 1248
  • essential: unknown other strains

Accession numbers[edit source | edit]

Phenotype[edit source | edit]

  • Share your knowledge and add information here. [edit]

DNA sequence[edit source | edit]

  • 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 source | edit]

General[edit source | edit]

  • locus tag: SACOL1083 [new locus tag: SACOL_RS05525 ]
  • symbol: PurD
  • description: phosphoribosylamine--glycine ligase
  • length: 415
  • theoretical pI: 4.89379
  • theoretical MW: 45858.9
  • GRAVY: -0.244819

Function[edit source | edit]

  • reaction:
    EC 6.3.4.13?  ExPASy
    Phosphoribosylamine--glycine ligaseATP + 5-phospho-D-ribosylamine + glycine = ADP + phosphate + N1-(5-phospho-D-ribosyl)glycinamide
  • TIGRFAM:
    MetabolismPurines, pyrimidines, nucleosides, and nucleotidesPurine ribonucleotide biosynthesisphosphoribosylamine--glycine ligase (TIGR00877; EC 6.3.4.13; HMM-score: 466)
    MetabolismPurines, pyrimidines, nucleosides, and nucleotidesPyrimidine ribonucleotide biosynthesiscarbamoyl-phosphate synthase, large subunit (TIGR01369; EC 6.3.5.5; HMM-score: 36.2)
    MetabolismPurines, pyrimidines, nucleosides, and nucleotidesPurine ribonucleotide biosynthesisphosphoribosylaminoimidazole carboxylase, ATPase subunit (TIGR01161; EC 4.1.1.21; HMM-score: 29.2)
    Cell structureCell envelopeBiosynthesis and degradation of murein sacculus and peptidoglycanD-alanine--D-alanine ligase (TIGR01205; EC 6.3.2.4; HMM-score: 28.3)
    Cellular processesCellular processesBiosynthesis of natural productscyanophycin synthetase (TIGR02068; EC 6.3.2.29,6.3.2.30; HMM-score: 24.7)
    MetabolismFatty acid and phospholipid metabolismBiosynthesisacetyl-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)
    MetabolismPurines, pyrimidines, nucleosides, and nucleotidesPurine ribonucleotide biosynthesisphosphoribosylglycinamide formyltransferase 2 (TIGR01142; EC 2.1.2.-; HMM-score: 19.4)
    MetabolismEnergy metabolismTCA cyclesuccinate-CoA ligase, beta subunit (TIGR01016; EC 6.2.1.-; HMM-score: 14.6)
    MetabolismEnergy metabolismGlycolysis/gluconeogenesispyruvate carboxylase (TIGR01235; EC 6.4.1.1; HMM-score: 14.2)
    MetabolismAmino acid biosynthesisOtherpyrrolysine biosynthesis protein PylC (TIGR03909; HMM-score: 13.7)
    lysine biosynthesis enzyme LysX (TIGR02144; HMM-score: 13.1)
  • TheSEED:  
    MiscellaneousMiscellaneous - no subcategoryEC 6.3.4.- Ligases that form carbon-nitrogen bonds Phosphoribosylamine--glycine ligase (EC 6.3.4.13) 
    Nucleosides and NucleotidesPurinesDe 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: 225.8)
    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 & interactions[edit source | edit]

  • domains:
  • modifications:
  • cofactors: Mg2+, Mn2+
  • effectors:
  • protein partners:
    SACOL1637(dnaK)molecular chaperone DnaK  [1] (data from MRSA252)
    SACOL1513(hup)DNA-binding protein HU  [1] (data from MRSA252)
    SACOL1102(pdhA)pyruvate dehydrogenase complex E1 component subunit alpha  [1] (data from MRSA252)
    SACOL1103(pdhB)pyruvate dehydrogenase complex E1 component subunit beta  [1] (data from MRSA252)
    SACOL1104(pdhC)branched-chain alpha-keto acid dehydrogenase E2  [1] (data from MRSA252)
    SACOL1105(pdhD)dihydrolipoamide dehydrogenase  [1] (data from MRSA252)
    SACOL1745(pyk)pyruvate kinase  [1] (data from MRSA252)
    SACOL0584(rplA)50S ribosomal protein L1  [1] (data from MRSA252)
    SACOL2236(rplB)50S ribosomal protein L2  [1] (data from MRSA252)
    SACOL2224(rplF)50S ribosomal protein L6  [1] (data from MRSA252)
    SACOL0585(rplJ)50S ribosomal protein L10  [1] (data from MRSA252)
    SACOL2220(rplO)50S ribosomal protein L15  [1] (data from MRSA252)
    SACOL1257(rplS)50S ribosomal protein L19  [1] (data from MRSA252)
    SACOL1702(rplU)50S ribosomal protein L21  [1] (data from MRSA252)
    SACOL2237(rplW)50S ribosomal protein L23  [1] (data from MRSA252)
    SACOL1769(rpsD)30S ribosomal protein S4  [1] (data from MRSA252)
    SACOL2222(rpsE)30S ribosomal protein S5  [1] (data from MRSA252)
    SACOL2206(rpsI)30S ribosomal protein S9  [1] (data from MRSA252)
    SACOL2214(rpsK)30S ribosomal protein S11  [1] (data from MRSA252)
    SACOL0594(tuf)elongation factor Tu  [1] (data from MRSA252)
    SACOL1753universal stress protein  [1] (data from MRSA252)
    SACOL2173alkaline shock protein 23  [1] (data from MRSA252)

Localization[edit source | edit]

  • 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
    • Ymax: 0.138
    • Ymax_pos: 42
    • Cmax: 0.117
    • Cmax_pos: 17
    • Smax: 0.286
    • Smax_pos: 35
    • Smean: 0.133
    • D: 0.136
  • predicted transmembrane helices (TMHMM): 0

Accession numbers[edit source | edit]

Protein sequence[edit source | edit]

  • MNVLVIGAGGREHALAYKLNQSNLVKQVFVIPGNEAMTPIAEVHTEISEPDHQAILDFAKRQNVDWVVIGPEQPLIDGLADILRANGFKVFGPNKQAAQIEGSKLFAKKIMEKYNIPTADYKEVERKKDALTYIENCELPVVVKKDGLAAGKGVIIADTIEAARSAIEIMYGDEEEGTVVFETFLEGEEFSLMTFVNGDLAVPFDCIAQDHKRAFDHDEGPNTGGMGAYCPVPHISDDVLKLTNETIAQPIAKAMLNEGYQFFGVLYIGAILTKDGPKVIEFNARFGDPEAQVLLSRMESDLMQHIIDLDEGKRTEFKWKNESIVGVMLASKGYPDAYEKGHKVSGFDLNENYFVSGLKKQGDTFVTSGGRVILAIGKGDNVQDAQRDAYKKVSQIQSDHLFYRHDIANKALQLK

Experimental data[edit source | edit]

  • experimentally validated: PeptideAtlas
    experimental localization: Cytoplasmic [2] [3] [4] [5]
    quantitative data / protein copy number per cell: 1731 [6]

Expression & Regulation[edit source | edit]

Operon[edit source | edit]

Regulation[edit source | edit]

  • sigma factor:
  • regulator:

Transcription pattern[edit source | edit]

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

Protein stability[edit source | edit]

  • half-life: 25.44 h [7]

Biological Material[edit source | edit]

Mutants[edit source | edit]

Expression vector[edit source | edit]

lacZ fusion[edit source | edit]

GFP fusion[edit source | edit]

two-hybrid system[edit source | edit]

FLAG-tag construct[edit source | edit]

Antibody[edit source | edit]

Other Information[edit source | edit]

You are kindly invited to share additional interesting facts.

Literature[edit source | edit]

References[edit source | edit]

  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)
  2. 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)
  3. 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)
  4. 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)
  5. 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)
  6. 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)
  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 source | edit]