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NCBI: 10-JUN-2013

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus COL
  • locus tag: SACOL1196 [new locus tag: SACOL_RS06125 ]
  • pan locus tag?: SAUPAN003453000
  • symbol: murD
  • pan gene symbol?: murD
  • synonym:
  • product: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SACOL1196 [new locus tag: SACOL_RS06125 ]
  • symbol: murD
  • product: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase
  • replicon: chromosome
  • strand: +
  • coordinates: 1201133..1202482
  • length: 1350
  • 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
    1261
    1321
    ATGCTTAATTATACAGGGTTAGAAAATAAAAATGTATTAGTTGTCGGTTTGGCAAAAAGT
    GGTTATGAAGCAGCTAAATTATTAAGTAAATTAGGTGCGAATGTAACTGTCAATGATGGA
    AAAGACTTATCACAAGATGCTCATGCAAAAGATTTAGAATCTATGGGCATTTCTGTTGTA
    AGTGGAAGTCATCCATTAACGTTGCTTGATAATAATCCAATAATTGTTAAAAATCCTGGA
    ATACCTTATACAGTATCTATTATTGATGAAGCAGTGAAACGAGGTTTGAAAATTTTAACA
    GAAGTTGAGTTAAGTTATCTAATCTCTGAAGCACCAATCATAGCTGTAACGGGTACAAAT
    GGTAAAACGACAGTTACTTCTCTAATTGGAGATATGTTTAAAAAAAGTCGCTTAACTGGA
    AGATTATCCGGCAATATTGGTTATGTTGCATCTAAAGTAGCACAAGAAGTAAAGCCTACA
    GATTATTTAGTTACAGAGTTGTCGTCATTCCAGTTACTTGGAATCGAAAAGTATAAACCA
    CACATTGCTATAATTACTAACATTTATTCGGCGCATCTAGATTACCATGAAAATTTAGAA
    AACTATCAAAATGCTAAAAAGCAAATATATAAAAATCAAACGGAAGAGGATTATTTGATT
    TGTAATTATCATCAAAGACAAGTGATAGAGTCGGAAGAATTAAAAGCTAAGACATTGTAT
    TTCTCAACTCAACAAGAAGTTGATGGTATTTATATTAAAGATGGTTTTATCGTTTATAAA
    GGTGTTCGTATTATTAACACTGAAGATCTAGTATTGCCTGGTGAACATAATTTAGAAAAT
    ATATTAGCAGCTGTGCTTGCTTGTATTTTAGCTGGTGTACCTATTAAAGCAATTATTGAT
    AGTTTAACTACATTTTCAGGAATAGAGCATAGATTGCAATATGTTGGTACTAATAGAACT
    AATAAATATTATAATGATTCCAAAGCAACAAACACGCTAGCAACACAGTTTGCCTTAAAT
    TCATTTAATCAACCAATCATTTGGTTATGTGGTGGTTTGGATCGAGGGAATGAATTTGAC
    GAACTCATTCCTTATATGGAAAATGTTCGCGCGATGGTTGTATTCGGACAAACGAAAGCT
    AAGTTTGCTAAACTAGGTAATAGTCAAGGGAAATCGGTCATTGAAGCGAACAATGTCGAA
    GACGCTGTTGATAAAGTACAAGATATTATAGAACCAAATGATGTTGTATTATTGTCACCT
    GCTTGTGCGAGTTGGGATCAATATAGTACTTTTGAAGAGCGTGGAGAGAAATTTATTGAA
    AGATTCCGTGCCCATTTACCATCTTATTAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    900
    960
    1020
    1080
    1140
    1200
    1260
    1320
    1350

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: SACOL1196 [new locus tag: SACOL_RS06125 ]
  • symbol: MurD
  • description: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase
  • length: 449
  • theoretical pI: 5.49171
  • theoretical MW: 49843.4
  • GRAVY: -0.167038

⊟Function[edit | edit source]

  • ⊞reaction:
    EC 6.3.2.9?  ExPASy
    UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase ATP + UDP-N-acetyl-alpha-D-muramoyl-L-alanine + D-glutamate = ADP + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate
  • ⊞TIGRFAM:
    Cell structure Cell envelope Biosynthesis and degradation of murein sacculus and peptidoglycan UDP-N-acetylmuramoylalanine--D-glutamate ligase (TIGR01087; EC 6.3.2.9; HMM-score: 415.2)
    and 10 more
    Cell structure Cell envelope Biosynthesis and degradation of murein sacculus and peptidoglycan UDP-N-acetylmuramate--L-alanine ligase (TIGR01082; EC 6.3.2.8; HMM-score: 131.2)
    Cell structure Cell envelope Biosynthesis and degradation of murein sacculus and peptidoglycan UDP-N-acetylmuramyl-tripeptide synthetase (TIGR01085; HMM-score: 86)
    Cell structure Cell envelope Biosynthesis and degradation of murein sacculus and peptidoglycan UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase (TIGR01143; EC 6.3.2.10; HMM-score: 83.6)
    Cell structure Cell envelope Biosynthesis and degradation of murein sacculus and peptidoglycan UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase (TIGR01081; HMM-score: 49.6)
    Cellular processes Cellular processes Biosynthesis of natural products cyanophycin synthetase (TIGR02068; EC 6.3.2.29,6.3.2.30; HMM-score: 34.3)
    Metabolism Amino acid biosynthesis Other pyrrolysine biosynthesis protein PylD (TIGR03911; HMM-score: 24.9)
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Folic acid bifunctional protein FolC (TIGR01499; EC 6.3.2.-; HMM-score: 17.7)
    Metabolism Energy metabolism Amino acids and amines alanine dehydrogenase (TIGR00518; EC 1.4.1.1; HMM-score: 13.9)
    3-hydroxybutyrate dehydrogenase (TIGR01963; HMM-score: 13.6)
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Heme, porphyrin, and cobalamin siroheme synthase, N-terminal domain (TIGR01470; HMM-score: 12.8)
  • ⊞TheSEED  :
    • UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase (EC 6.3.2.9)
    Cell Wall and Capsule Cell Wall and Capsule - no subcategory Peptidoglycan Biosynthesis  UDP-N-acetylmuramoylalanine--D-glutamate ligase (EC 6.3.2.9)
    and 1 more
    Cell Wall and Capsule Cell Wall and Capsule - no subcategory Peptidoglycan biosynthesis--gjo  UDP-N-acetylmuramoylalanine--D-glutamate ligase (EC 6.3.2.9)
  • ⊞PFAM:
    P-loop_NTPase (CL0023) Mur_ligase_M; Mur ligase middle domain (PF08245; HMM-score: 113.2)
    and 8 more
    Mur_ligase_C_sf (CL0794) Mur_ligase_C; Mur ligase, glutamate ligase domain (PF02875; HMM-score: 48.6)
    MurF-HprK_N (CL0365) MurD-like_N; Mur ligase MurD-like, N-terminal domain (PF21799; HMM-score: 33.8)
    NADP_Rossmann (CL0063) Pyr_redox; Pyridine nucleotide-disulphide oxidoreductase (PF00070; HMM-score: 16.2)
    Shikimate_DH; Shikimate / quinate 5-dehydrogenase (PF01488; HMM-score: 15.8)
    Pyr_redox_3; Pyridine nucleotide-disulphide oxidoreductase (PF13738; HMM-score: 15.5)
    2-Hacid_dh_C; D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain (PF02826; HMM-score: 15.4)
    AlaDh_PNT_C; Alanine dehydrogenase/PNT, C-terminal domain (PF01262; HMM-score: 14.3)
    NAD_binding_7; Putative NAD(P)-binding (PF13241; HMM-score: 12.8)

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

  • domains:
  • modifications:
  • cofactors:
  • effectors:

⊟Localization[edit | edit source]

  • ⊞PSORTb: Cytoplasmic
    • Cytoplasmic Score: 9.97
    • Cytoplasmic Membrane Score: 0
    • Cellwall Score: 0.01
    • Extracellular Score: 0.02
    • Internal Helices: 0
  • ⊞DeepLocPro: Cytoplasmic
    • Cytoplasmic Score: 0.9914
    • Cytoplasmic Membrane Score: 0.0022
    • Cell wall & surface Score: 0.0012
    • Extracellular Score: 0.0052
  • ⊞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): 0.019906
    • TAT(Tat/SPI): 0.00131
    • LIPO(Sec/SPII): 0.001645
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MLNYTGLENKNVLVVGLAKSGYEAAKLLSKLGANVTVNDGKDLSQDAHAKDLESMGISVVSGSHPLTLLDNNPIIVKNPGIPYTVSIIDEAVKRGLKILTEVELSYLISEAPIIAVTGTNGKTTVTSLIGDMFKKSRLTGRLSGNIGYVASKVAQEVKPTDYLVTELSSFQLLGIEKYKPHIAIITNIYSAHLDYHENLENYQNAKKQIYKNQTEEDYLICNYHQRQVIESEELKAKTLYFSTQQEVDGIYIKDGFIVYKGVRIINTEDLVLPGEHNLENILAAVLACILAGVPIKAIIDSLTTFSGIEHRLQYVGTNRTNKYYNDSKATNTLATQFALNSFNQPIIWLCGGLDRGNEFDELIPYMENVRAMVVFGQTKAKFAKLGNSQGKSVIEANNVEDAVDKVQDIIEPNDVVLLSPACASWDQYSTFEERGEKFIERFRAHLPSY

⊟Experimental data[edit | edit source]

  • experimentally validated: PeptideAtlas
  • protein localization: Cytoplasmic [1] [2] [3]
  • quantitative data / protein copy number per cell: 184 [4]
  • ⊟interaction partners:
    SACOL1745(pyk)pyruvate kinase  [5] (data from MRSA252)
    SACOL0585(rplJ)50S ribosomal protein L10  [5] (data from MRSA252)
    SACOL0731LysR family transcriptional regulator  [5] (data from MRSA252)

⊟Expression & Regulation[edit | edit source]

⊟Operon[edit | edit source]

⊟Regulation[edit | edit source]

  • regulator:

⊟Transcription pattern[edit | edit source]

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

⊟Protein stability[edit | edit source]

  • half-life: 56.17 h [6]

⊞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. ↑ 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)
  2. ↑ 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)
  3. ↑ 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)
  4. ↑ 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)
  5. ↑ Jump up to: 5.0 5.1 5.2 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)
  6. ↑ 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 | edit source]

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