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Q8ZAR2

- PUR2_YERPE

UniProt

Q8ZAR2 - PUR2_YERPE

Protein

Phosphoribosylamine--glycine ligase

Gene

purD

Organism
Yersinia pestis
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 99 (01 Oct 2014)
      Sequence version 1 (27 Mar 2002)
      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 bindingi286 – 2861Magnesium or manganeseUniRule annotation
    Metal bindingi288 – 2881Magnesium or manganeseUniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi135 – 19662ATPUniRule 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

    BioCyciYPES214092:GKDD-3692-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:YPO3729, y0501, YP_3092
    OrganismiYersinia pestis
    Taxonomic identifieri632 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeYersinia
    ProteomesiUP000000815: Chromosome, UP000001019: Chromosome, UP000002490: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 428428Phosphoribosylamine--glycine ligasePRO_0000151506Add
    BLAST

    Proteomic databases

    PRIDEiQ8ZAR2.

    Interactioni

    Protein-protein interaction databases

    IntActiQ8ZAR2. 6 interactions.
    STRINGi214092.YPO3729.

    Structurei

    Secondary structure

    428
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi1 – 77
    Helixi10 – 1910
    Beta strandi25 – 328
    Helixi35 – 395
    Helixi53 – 6210
    Beta strandi65 – 706
    Helixi73 – 775
    Helixi80 – 867
    Beta strandi91 – 933
    Helixi96 – 1038
    Helixi105 – 11410
    Beta strandi122 – 1265
    Helixi128 – 13811
    Beta strandi140 – 14910
    Beta strandi154 – 1585
    Helixi161 – 17212
    Helixi175 – 1784
    Beta strandi184 – 1885
    Beta strandi192 – 20413
    Beta strandi206 – 2083
    Beta strandi212 – 2143
    Beta strandi217 – 2193
    Turni220 – 2223
    Beta strandi223 – 2264
    Beta strandi230 – 2356
    Helixi241 – 25010
    Helixi252 – 26110
    Beta strandi267 – 27610
    Beta strandi282 – 2876
    Helixi289 – 2913
    Turni293 – 2953
    Helixi296 – 3027
    Helixi307 – 3159
    Helixi319 – 3213
    Beta strandi331 – 3388
    Turni339 – 3424
    Beta strandi362 – 37110
    Beta strandi377 – 3793
    Beta strandi381 – 39010
    Helixi394 – 40512
    Helixi421 – 4244
    Turni425 – 4273

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3MJFX-ray1.47A1-428[»]
    ProteinModelPortaliQ8ZAR2.
    SMRiQ8ZAR2. Positions 1-426.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ8ZAR2.

    Family & Domainsi

    Domains and Repeats

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

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiCOG0151.
    HOGENOMiHOG000033463.
    KOiK01945.
    OMAiDIHWDGS.
    OrthoDBiEOG69SKD1.

    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.

    Q8ZAR2-1 [UniParc]FASTAAdd to Basket

    « Hide

    MNILIIGNGG REHALGWKAA QSPLADKIYV APGNAGTALE PTLENVDIAA    50
    TDIAGLLAFA QSHDIGLTIV GPEAPLVIGV VDAFRAAGLA IFGPTQAAAQ 100
    LEGSKAFTKD FLARHNIPSA EYQNFTDVEA ALAYVRQKGA PIVIKADGLA 150
    AGKGVIVAMT QEEAETAVND MLAGNAFGDA GHRIVVEEFL DGEEASFIVM 200
    VDGENVLPMA TSQDHKRVGD GDTGPNTGGM GAYSPAPVVT DDVHQRVMDQ 250
    VIWPTVRGMA AEGNIYTGFL YAGLMISADG QPKVIEFNCR FGDPETQPIM 300
    LRMRSDLVEL CLAGTQGKLN EKTSDWDERP SLGVVLAAGG YPADYRQGDV 350
    IHGLPQQEVK DGKVFHAGTK LNGNHEVVTN GGRVLCVTAL GETVAQAQQY 400
    AYQLAEGIQW EGVFCRKDIG YRAIARGK 428
    Length:428
    Mass (Da):45,317
    Last modified:March 27, 2002 - v1
    Checksum:i0D12863DD2424EFF
    GO

    Sequence cautioni

    The sequence AAM84090.1 differs from that shown. Reason: Erroneous initiation.
    The sequence AAS63262.1 differs from that shown. Reason: Erroneous initiation.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AL590842 Genomic DNA. Translation: CAL22316.1.
    AE009952 Genomic DNA. Translation: AAM84090.1. Different initiation.
    AE017042 Genomic DNA. Translation: AAS63262.1. Different initiation.
    PIRiAI0453.
    RefSeqiNP_667839.1. NC_004088.1.
    NP_994385.1. NC_005810.1.
    YP_002348609.1. NC_003143.1.

    Genome annotation databases

    EnsemblBacteriaiAAM84090; AAM84090; y0501.
    AAS63262; AAS63262; YP_3092.
    GeneIDi1145448.
    1176555.
    2765674.
    KEGGiype:YPO3729.
    ypk:y0501.
    ypm:YP_3092.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AL590842 Genomic DNA. Translation: CAL22316.1 .
    AE009952 Genomic DNA. Translation: AAM84090.1 . Different initiation.
    AE017042 Genomic DNA. Translation: AAS63262.1 . Different initiation.
    PIRi AI0453.
    RefSeqi NP_667839.1. NC_004088.1.
    NP_994385.1. NC_005810.1.
    YP_002348609.1. NC_003143.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3MJF X-ray 1.47 A 1-428 [» ]
    ProteinModelPortali Q8ZAR2.
    SMRi Q8ZAR2. Positions 1-426.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi Q8ZAR2. 6 interactions.
    STRINGi 214092.YPO3729.

    Proteomic databases

    PRIDEi Q8ZAR2.

    Protocols and materials databases

    DNASUi 1145448.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAM84090 ; AAM84090 ; y0501 .
    AAS63262 ; AAS63262 ; YP_3092 .
    GeneIDi 1145448.
    1176555.
    2765674.
    KEGGi ype:YPO3729.
    ypk:y0501.
    ypm:YP_3092.

    Phylogenomic databases

    eggNOGi COG0151.
    HOGENOMi HOG000033463.
    KOi K01945.
    OMAi DIHWDGS.
    OrthoDBi EOG69SKD1.

    Enzyme and pathway databases

    UniPathwayi UPA00074 ; UER00125 .
    BioCyci YPES214092:GKDD-3692-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei Q8ZAR2.

    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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: CO-92 / Biovar Orientalis.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: KIM10+ / Biovar Mediaevalis.
    3. "Complete genome sequence of Yersinia pestis strain 91001, an isolate avirulent to humans."
      Song Y., Tong Z., Wang J., Wang L., Guo Z., Han Y., Zhang J., Pei D., Zhou D., Qin H., Pang X., Han Y., Zhai J., Li M., Cui B., Qi Z., Jin L., Dai R.
      , Chen F., Li S., Ye C., Du Z., Lin W., Wang J., Yu J., Yang H., Wang J., Huang P., Yang R.
      DNA Res. 11:179-197(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: 91001 / Biovar Mediaevalis.

    Entry informationi

    Entry nameiPUR2_YERPE
    AccessioniPrimary (citable) accession number: Q8ZAR2
    Secondary accession number(s): Q0WAS9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 27, 2002
    Last sequence update: March 27, 2002
    Last modified: October 1, 2014
    This is version 99 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. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3