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P15640

- PUR2_ECOLI

UniProt

P15640 - PUR2_ECOLI

Protein

Phosphoribosylamine--glycine ligase

Gene

purD

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 132 (01 Oct 2014)
      Sequence version 2 (01 Oct 1993)
      Previous versions | rss
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    Functioni

    Catalytic activityi

    ATP + 5-phospho-D-ribosylamine + glycine = ADP + phosphate + N(1)-(5-phospho-D-ribosyl)glycinamide.

    Cofactori

    Binds 1 magnesium or manganese ion per subunit.By similarity

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi286 – 2861Magnesium or manganeseBy similarity
    Metal bindingi288 – 2881Magnesium or manganeseBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi135 – 19662ATPBy similarityAdd
    BLAST

    GO - Molecular functioni

    1. ATPase activity, coupled Source: EcoliWiki
    2. ATP binding Source: EcoliWiki
    3. magnesium ion binding Source: UniProtKB-HAMAP
    4. manganese ion binding Source: UniProtKB-HAMAP
    5. phosphoribosylamine-glycine ligase activity Source: EcoCyc

    GO - Biological processi

    1. 'de novo' IMP biosynthetic process Source: UniProtKB-UniPathway
    2. ATP catabolic process Source: GOC
    3. cellular response to DNA damage stimulus Source: EcoliWiki
    4. purine nucleobase biosynthetic process Source: InterPro
    5. purine nucleotide biosynthetic process Source: EcoliWiki

    Keywords - Molecular functioni

    Ligase

    Keywords - Biological processi

    Purine biosynthesis

    Keywords - Ligandi

    ATP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:GLYCRIBONUCSYN-MONOMER.
    ECOL316407:JW3969-MONOMER.
    MetaCyc:GLYCRIBONUCSYN-MONOMER.
    UniPathwayiUPA00074; UER00125.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Phosphoribosylamine--glycine ligase (EC:6.3.4.13)
    Alternative name(s):
    GARS
    Glycinamide ribonucleotide synthetase
    Phosphoribosylglycinamide synthetase
    Gene namesi
    Name:purD
    Ordered Locus Names:b4005, JW3969
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10792. purD.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 429429Phosphoribosylamine--glycine ligasePRO_0000151448Add
    BLAST

    Proteomic databases

    PaxDbiP15640.
    PRIDEiP15640.

    2D gel databases

    SWISS-2DPAGEP15640.

    Expressioni

    Gene expression databases

    GenevestigatoriP15640.

    Interactioni

    Subunit structurei

    Monomer.

    Protein-protein interaction databases

    IntActiP15640. 4 interactions.
    STRINGi511145.b4005.

    Structurei

    Secondary structure

    429
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi1 – 77
    Helixi10 – 1910
    Beta strandi25 – 328
    Helixi35 – 395
    Beta strandi43 – 453
    Helixi53 – 6210
    Beta strandi66 – 705
    Helixi73 – 775
    Helixi80 – 867
    Beta strandi91 – 933
    Turni96 – 994
    Helixi100 – 1034
    Helixi105 – 11410
    Beta strandi122 – 1298
    Helixi130 – 1389
    Beta strandi140 – 1456
    Beta strandi155 – 1606
    Helixi161 – 1688
    Turni169 – 1724
    Beta strandi184 – 1885
    Beta strandi192 – 20413
    Beta strandi206 – 21914
    Turni220 – 2223
    Beta strandi223 – 23513
    Helixi241 – 25010
    Helixi252 – 26110
    Beta strandi267 – 27711
    Beta strandi282 – 2909
    Turni293 – 2953
    Helixi296 – 3027
    Helixi307 – 3159
    Helixi319 – 3213
    Beta strandi328 – 33811
    Turni339 – 3424
    Beta strandi362 – 37110
    Beta strandi377 – 3793
    Beta strandi381 – 39313
    Helixi394 – 40411
    Turni405 – 4073
    Helixi421 – 4255

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1GSOX-ray1.60A1-429[»]
    ProteinModelPortaliP15640.
    SMRiP15640. Positions 1-426.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP15640.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini109 – 316208ATP-graspAdd
    BLAST

    Sequence similaritiesi

    Belongs to the GARS family.Curated
    Contains 1 ATP-grasp domain.Curated

    Phylogenomic databases

    eggNOGiCOG0151.
    HOGENOMiHOG000033463.
    KOiK01945.
    OMAiYKGFLYA.
    OrthoDBiEOG69SKD1.
    PhylomeDBiP15640.

    Family and domain databases

    Gene3Di3.30.1490.20. 1 hit.
    3.30.470.20. 1 hit.
    3.40.50.20. 1 hit.
    3.90.600.10. 1 hit.
    HAMAPiMF_00138. GARS.
    InterProiIPR011761. ATP-grasp.
    IPR013815. ATP_grasp_subdomain_1.
    IPR013816. ATP_grasp_subdomain_2.
    IPR016185. PreATP-grasp_dom.
    IPR020561. PRibGlycinamid_synth_ATP-grasp.
    IPR000115. PRibGlycinamide_synth.
    IPR020560. PRibGlycinamide_synth_C-dom.
    IPR020559. PRibGlycinamide_synth_CS.
    IPR020562. PRibGlycinamide_synth_N.
    IPR011054. Rudment_hybrid_motif.
    [Graphical view]
    PfamiPF01071. GARS_A. 1 hit.
    PF02843. GARS_C. 1 hit.
    PF02844. GARS_N. 1 hit.
    [Graphical view]
    SUPFAMiSSF51246. SSF51246. 1 hit.
    SSF52440. SSF52440. 1 hit.
    TIGRFAMsiTIGR00877. purD. 1 hit.
    PROSITEiPS50975. ATP_GRASP. 1 hit.
    PS00184. GARS. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P15640-1 [UniParc]FASTAAdd to Basket

    « Hide

    MKVLVIGNGG REHALAWKAA QSPLVETVFV APGNAGTALE PALQNVAIGV    50
    TDIPALLDFA QNEKIDLTIV GPEAPLVKGV VDTFRAAGLK IFGPTAGAAQ 100
    LEGSKAFTKD FLARHKIPTA EYQNFTEVEP ALAYLREKGA PIVIKADGLA 150
    AGKGVIVAMT LEEAEAAVHD MLAGNAFGDA GHRIVIEEFL DGEEASFIVM 200
    VDGEHVLPMA TSQDHKRVGD KDTGPNTGGM GAYSPAPVVT DDVHQRTMER 250
    IIWPTVKGMA AEGNTYTGFL YAGLMIDKQG NPKVIEFNCR FGDPETQPIM 300
    LRMKSDLVEL CLAACESKLD EKTSEWDERA SLGVVMAAGG YPGDYRTGDV 350
    IHGLPLEEVA GGKVFHAGTK LADDEQVVTN GGRVLCVTAL GHTVAEAQKR 400
    AYALMTDIHW DDCFCRKDIG WRAIEREQN 429
    Length:429
    Mass (Da):45,940
    Last modified:October 1, 1993 - v2
    Checksum:i5E9EFAD478BC1FF4
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti15 – 162LA → WR in AAA24455. (PubMed:2687276)Curated
    Sequence conflicti97 – 971G → V in AAA24455. (PubMed:2687276)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J05126 Genomic DNA. Translation: AAA24455.1.
    X51950 Genomic DNA. Translation: CAA36213.1.
    U00006 Genomic DNA. Translation: AAC43103.1.
    U00096 Genomic DNA. Translation: AAC76979.1.
    AP009048 Genomic DNA. Translation: BAE77314.1.
    PIRiA33771. AJECQG.
    RefSeqiNP_418433.1. NC_000913.3.
    YP_491455.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC76979; AAC76979; b4005.
    BAE77314; BAE77314; BAE77314.
    GeneIDi12933468.
    948504.
    KEGGiecj:Y75_p3191.
    eco:b4005.
    PATRICi32123535. VBIEscCol129921_4120.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J05126 Genomic DNA. Translation: AAA24455.1 .
    X51950 Genomic DNA. Translation: CAA36213.1 .
    U00006 Genomic DNA. Translation: AAC43103.1 .
    U00096 Genomic DNA. Translation: AAC76979.1 .
    AP009048 Genomic DNA. Translation: BAE77314.1 .
    PIRi A33771. AJECQG.
    RefSeqi NP_418433.1. NC_000913.3.
    YP_491455.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1GSO X-ray 1.60 A 1-429 [» ]
    ProteinModelPortali P15640.
    SMRi P15640. Positions 1-426.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi P15640. 4 interactions.
    STRINGi 511145.b4005.

    2D gel databases

    SWISS-2DPAGE P15640.

    Proteomic databases

    PaxDbi P15640.
    PRIDEi P15640.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC76979 ; AAC76979 ; b4005 .
    BAE77314 ; BAE77314 ; BAE77314 .
    GeneIDi 12933468.
    948504.
    KEGGi ecj:Y75_p3191.
    eco:b4005.
    PATRICi 32123535. VBIEscCol129921_4120.

    Organism-specific databases

    EchoBASEi EB0785.
    EcoGenei EG10792. purD.

    Phylogenomic databases

    eggNOGi COG0151.
    HOGENOMi HOG000033463.
    KOi K01945.
    OMAi YKGFLYA.
    OrthoDBi EOG69SKD1.
    PhylomeDBi P15640.

    Enzyme and pathway databases

    UniPathwayi UPA00074 ; UER00125 .
    BioCyci EcoCyc:GLYCRIBONUCSYN-MONOMER.
    ECOL316407:JW3969-MONOMER.
    MetaCyc:GLYCRIBONUCSYN-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P15640.
    PROi P15640.

    Gene expression databases

    Genevestigatori P15640.

    Family and domain databases

    Gene3Di 3.30.1490.20. 1 hit.
    3.30.470.20. 1 hit.
    3.40.50.20. 1 hit.
    3.90.600.10. 1 hit.
    HAMAPi MF_00138. GARS.
    InterProi IPR011761. ATP-grasp.
    IPR013815. ATP_grasp_subdomain_1.
    IPR013816. ATP_grasp_subdomain_2.
    IPR016185. PreATP-grasp_dom.
    IPR020561. PRibGlycinamid_synth_ATP-grasp.
    IPR000115. PRibGlycinamide_synth.
    IPR020560. PRibGlycinamide_synth_C-dom.
    IPR020559. PRibGlycinamide_synth_CS.
    IPR020562. PRibGlycinamide_synth_N.
    IPR011054. Rudment_hybrid_motif.
    [Graphical view ]
    Pfami PF01071. GARS_A. 1 hit.
    PF02843. GARS_C. 1 hit.
    PF02844. GARS_N. 1 hit.
    [Graphical view ]
    SUPFAMi SSF51246. SSF51246. 1 hit.
    SSF52440. SSF52440. 1 hit.
    TIGRFAMsi TIGR00877. purD. 1 hit.
    PROSITEi PS50975. ATP_GRASP. 1 hit.
    PS00184. GARS. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Nucleotide sequence analysis of genes purH and purD involved in the de novo purine nucleotide biosynthesis of Escherichia coli."
      Aiba A., Mizobuchi K.
      J. Biol. Chem. 264:21239-21246(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Glycinamide ribonucleotide synthetase from Escherichia coli: cloning, overproduction, sequencing, isolation, and characterization."
      Shen Y., Rudolph J., Stern M., Flannigan K.A., Smith J.M.
      Biochemistry 29:218-227(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    3. "Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes."
      Blattner F.R., Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L.
      Nucleic Acids Res. 21:5408-5417(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    5. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    6. "X-ray crystal structure of glycinamide ribonucleotide synthetase from Escherichia coli."
      Wang W., Kappock T.J., Stubbe J., Ealick S.E.
      Biochemistry 37:15647-15662(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).

    Entry informationi

    Entry nameiPUR2_ECOLI
    AccessioniPrimary (citable) accession number: P15640
    Secondary accession number(s): Q2M8U2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 1, 1990
    Last sequence update: October 1, 1993
    Last modified: October 1, 2014
    This is version 132 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3