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Protein

Phosphoribosylamine--glycine ligase

Gene

purD

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

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

Cofactori

Mg2+By similarity, Mn2+By similarityNote: Binds 1 Mg(2+) or Mn2+ 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-HAMAP
  2. purine nucleobase biosynthetic process Source: InterPro
Complete GO annotation...

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

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
InParanoidiP12039.
KOiK01945.
OMAiENLECEH.
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

        10         20         30         40         50
MNVLIIGKGG REHTLAWKAA QSSLVENVFA APGNDGMAAS AQLVNIEESD
60 70 80 90 100
HAGLVSFAKQ NQVGLTIVGP EVPLIEGLVD EFEKAGLHVF GPSKAAAIIE
110 120 130 140 150
GSKQFAKDLM KKYDIPTAEY ETFTSFDEAK AYVQEKGAPI VIKADGLAAG
160 170 180 190 200
KGVTVAMTEE EAIACLHDFL EDEKFGDASA SVVIEEYLSG EEFSLMAFVK
210 220 230 240 250
GEKVYPMVIA QDHKRAFDGD KGPNTGGMGA YSPVPQISEE TVRHAVETIV
260 270 280 290 300
KPAAKAMVQE GRSFTGVLYA GLMLTENGSK VIEFNARFGD PETQVVLPRM
310 320 330 340 350
ESDLVQVLLD LLDDKEVDLR WKDTAAVSVV LASEGYPESY AKGTPIGSLA
360 370 380 390 400
AETEQVVVFH AGTKAEGGEF VTNGGRVANV TAFDETFEAA RDRVYKAVDE
410 420
IFKPGLFFRK DIGARALKAA QK
Length:422
Mass (Da):45,280
Last modified:October 1, 1989 - v1
Checksum:i4EF390A85CC90FB2
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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_JNCM01000032.1.

Genome annotation databases

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

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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_JNCM01000032.1.

3D structure databases

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

Protein-protein interaction databases

STRINGi224308.BSU06530.

Proteomic databases

PaxDbiP12039.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

GenoListiBSU06530. [Micado]

Phylogenomic databases

eggNOGiCOG0151.
HOGENOMiHOG000033463.
InParanoidiP12039.
KOiK01945.
OMAiENLECEH.
OrthoDBiEOG69SKD1.
PhylomeDBiP12039.

Enzyme and pathway databases

UniPathwayiUPA00074; UER00125.
BioCyciBSUB:BSU06530-MONOMER.

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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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: January 7, 2015
This is version 117 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.