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P15640

- PUR2_ECOLI

UniProt

P15640 - PUR2_ECOLI

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Protein

Phosphoribosylamine--glycine ligase

Gene

purD

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 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.

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
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

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.
InParanoidiP15640.
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

        10         20         30         40         50
MKVLVIGNGG REHALAWKAA QSPLVETVFV APGNAGTALE PALQNVAIGV
60 70 80 90 100
TDIPALLDFA QNEKIDLTIV GPEAPLVKGV VDTFRAAGLK IFGPTAGAAQ
110 120 130 140 150
LEGSKAFTKD FLARHKIPTA EYQNFTEVEP ALAYLREKGA PIVIKADGLA
160 170 180 190 200
AGKGVIVAMT LEEAEAAVHD MLAGNAFGDA GHRIVIEEFL DGEEASFIVM
210 220 230 240 250
VDGEHVLPMA TSQDHKRVGD KDTGPNTGGM GAYSPAPVVT DDVHQRTMER
260 270 280 290 300
IIWPTVKGMA AEGNTYTGFL YAGLMIDKQG NPKVIEFNCR FGDPETQPIM
310 320 330 340 350
LRMKSDLVEL CLAACESKLD EKTSEWDERA SLGVVMAAGG YPGDYRTGDV
360 370 380 390 400
IHGLPLEEVA GGKVFHAGTK LADDEQVVTN GGRVLCVTAL GHTVAEAQKR
410 420
AYALMTDIHW DDCFCRKDIG WRAIEREQN
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.
InParanoidi P15640.
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

« Hide 'large scale' publications
  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 29, 2014
This is version 133 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