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P12039

- PUR2_BACSU

UniProt

P12039 - PUR2_BACSU

Protein

Phosphoribosylamine--glycine ligase

Gene

purD

Organism
Bacillus subtilis (strain 168)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 114 (01 Oct 2014)
      Sequence version 1 (01 Oct 1989)
      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.UniRule annotation

    Cofactori

    Binds 1 magnesium or manganese ion per subunit.By similarity

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi283 – 2831Magnesium or manganeseUniRule annotation
    Metal bindingi285 – 2851Magnesium or manganeseUniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi133 – 19462ATPUniRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-HAMAP
    2. magnesium ion binding Source: UniProtKB-HAMAP
    3. manganese ion binding Source: UniProtKB-HAMAP
    4. phosphoribosylamine-glycine ligase activity Source: UniProtKB-HAMAP

    GO - Biological processi

    1. 'de novo' IMP biosynthetic process Source: UniProtKB-UniPathway
    2. purine nucleobase biosynthetic process Source: InterPro

    Keywords - Molecular functioni

    Ligase

    Keywords - Biological processi

    Purine biosynthesis

    Keywords - Ligandi

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

    Enzyme and pathway databases

    BioCyciBSUB:BSU06530-MONOMER.
    UniPathwayiUPA00074; UER00125.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Phosphoribosylamine--glycine ligaseUniRule annotation (EC:6.3.4.13UniRule annotation)
    Alternative name(s):
    GARSUniRule annotation
    Glycinamide ribonucleotide synthetaseUniRule annotation
    Phosphoribosylglycinamide synthetaseUniRule annotation
    Gene namesi
    Name:purDUniRule annotation
    Ordered Locus Names:BSU06530
    OrganismiBacillus subtilis (strain 168)
    Taxonomic identifieri224308 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    ProteomesiUP000001570: Chromosome

    Organism-specific databases

    GenoListiBSU06530. [Micado]

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 422422Phosphoribosylamine--glycine ligasePRO_0000151436Add
    BLAST

    Proteomic databases

    PaxDbiP12039.

    Interactioni

    Protein-protein interaction databases

    STRINGi224308.BSU06530.

    Structurei

    Secondary structure

    1
    422
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi2 – 76
    Helixi10 – 1910
    Beta strandi26 – 327
    Helixi35 – 373
    Turni38 – 403
    Helixi51 – 6010
    Beta strandi63 – 686
    Helixi71 – 755
    Helixi78 – 847
    Beta strandi89 – 913
    Turni94 – 974
    Helixi98 – 1014
    Helixi103 – 11210
    Beta strandi120 – 1245
    Helixi126 – 13611
    Beta strandi138 – 1469
    Helixi148 – 1503
    Beta strandi153 – 1586
    Helixi159 – 17012
    Helixi176 – 1794
    Beta strandi180 – 1867
    Beta strandi190 – 20011
    Beta strandi203 – 2064
    Beta strandi210 – 2178
    Helixi218 – 2203
    Beta strandi221 – 23313
    Helixi239 – 24810
    Helixi250 – 25910
    Beta strandi265 – 27511
    Beta strandi278 – 28710
    Turni290 – 2923
    Helixi293 – 2964
    Helixi297 – 2993
    Helixi304 – 3129
    Beta strandi325 – 3339
    Turni334 – 3374
    Beta strandi345 – 3473
    Beta strandi353 – 36513
    Beta strandi367 – 3726
    Beta strandi374 – 38613
    Helixi387 – 40115
    Helixi414 – 4207

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2XCLX-ray2.10A1-422[»]
    2XD4X-ray2.65A1-422[»]
    ProteinModelPortaliP12039.
    SMRiP12039. Positions 1-421.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini107 – 313207ATP-graspUniRule annotationAdd
    BLAST

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiCOG0151.
    HOGENOMiHOG000033463.
    KOiK01945.
    OMAiYKGFLYA.
    OrthoDBiEOG69SKD1.
    PhylomeDBiP12039.

    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.

    P12039-1 [UniParc]FASTAAdd to Basket

    « Hide

    MNVLIIGKGG REHTLAWKAA QSSLVENVFA APGNDGMAAS AQLVNIEESD    50
    HAGLVSFAKQ NQVGLTIVGP EVPLIEGLVD EFEKAGLHVF GPSKAAAIIE 100
    GSKQFAKDLM KKYDIPTAEY ETFTSFDEAK AYVQEKGAPI VIKADGLAAG 150
    KGVTVAMTEE EAIACLHDFL EDEKFGDASA SVVIEEYLSG EEFSLMAFVK 200
    GEKVYPMVIA QDHKRAFDGD KGPNTGGMGA YSPVPQISEE TVRHAVETIV 250
    KPAAKAMVQE GRSFTGVLYA GLMLTENGSK VIEFNARFGD PETQVVLPRM 300
    ESDLVQVLLD LLDDKEVDLR WKDTAAVSVV LASEGYPESY AKGTPIGSLA 350
    AETEQVVVFH AGTKAEGGEF VTNGGRVANV TAFDETFEAA RDRVYKAVDE 400
    IFKPGLFFRK DIGARALKAA QK 422
    Length:422
    Mass (Da):45,280
    Last modified:October 1, 1989 - v1
    Checksum:i4EF390A85CC90FB2
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J02732 Genomic DNA. Translation: AAA22684.1.
    AF011544 Genomic DNA. Translation: AAB72186.1.
    AL009126 Genomic DNA. Translation: CAB12473.1.
    PIRiB29183. AJBSAG.
    RefSeqiNP_388535.1. NC_000964.3.
    WP_003242993.1. NZ_CM000487.1.

    Genome annotation databases

    EnsemblBacteriaiCAB12473; CAB12473; BSU06530.
    GeneIDi938741.
    KEGGibsu:BSU06530.
    PATRICi18972948. VBIBacSub10457_0688.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J02732 Genomic DNA. Translation: AAA22684.1 .
    AF011544 Genomic DNA. Translation: AAB72186.1 .
    AL009126 Genomic DNA. Translation: CAB12473.1 .
    PIRi B29183. AJBSAG.
    RefSeqi NP_388535.1. NC_000964.3.
    WP_003242993.1. NZ_CM000487.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2XCL X-ray 2.10 A 1-422 [» ]
    2XD4 X-ray 2.65 A 1-422 [» ]
    ProteinModelPortali P12039.
    SMRi P12039. Positions 1-421.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 224308.BSU06530.

    Proteomic databases

    PaxDbi P12039.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai CAB12473 ; CAB12473 ; BSU06530 .
    GeneIDi 938741.
    KEGGi bsu:BSU06530.
    PATRICi 18972948. VBIBacSub10457_0688.

    Organism-specific databases

    GenoListi BSU06530. [Micado ]

    Phylogenomic databases

    eggNOGi COG0151.
    HOGENOMi HOG000033463.
    KOi K01945.
    OMAi YKGFLYA.
    OrthoDBi EOG69SKD1.
    PhylomeDBi P12039.

    Enzyme and pathway databases

    UniPathwayi UPA00074 ; UER00125 .
    BioCyci BSUB:BSU06530-MONOMER.

    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. "Cloning and characterization of a 12-gene cluster from Bacillus subtilis encoding nine enzymes for de novo purine nucleotide synthesis."
      Ebbole D.J., Zalkin H.
      J. Biol. Chem. 262:8274-8287(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "The 52 degrees-55 degrees segment of the Bacillus subtilis chromosome: a region devoted to purine uptake and metabolism, and containing the genes cotA, gabP and guaA and the pur gene cluster within a 34960 bp nucleotide sequence."
      Borriss R., Porwollik S., Schroeter R.
      Microbiology 142:3027-3031(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: 168.
    3. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
      Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
      , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
      Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: 168.

    Entry informationi

    Entry nameiPUR2_BACSU
    AccessioniPrimary (citable) accession number: P12039
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1989
    Last sequence update: October 1, 1989
    Last modified: October 1, 2014
    This is version 114 of the entry and version 1 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. Bacillus subtilis
      Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
    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