Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Phosphoribosylamine--glycine ligase

Gene

purD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 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

Mg2+By similarity, Mn2+By similarityNote: Binds 1 Mg(2+) or Mn2+ ion per subunit.By similarity

Pathway: IMP biosynthesis via de novo pathway

This protein is involved in step 2 of the subpathway that synthesizes N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-alpha-D-ribose 1-diphosphate.
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. Amidophosphoribosyltransferase (purF), Amidophosphoribosyltransferase (purF)
  2. Phosphoribosylamine--glycine ligase (purD), Phosphoribosylamine--glycine ligase (purD)
This subpathway is part of the pathway IMP biosynthesis via de novo pathway, which is itself part of Purine metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-alpha-D-ribose 1-diphosphate, the pathway IMP biosynthesis via de novo pathway and in Purine metabolism.

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

  • ATPase activity, coupled Source: EcoliWiki
  • ATP binding Source: EcoliWiki
  • magnesium ion binding Source: UniProtKB-HAMAP
  • manganese ion binding Source: UniProtKB-HAMAP
  • phosphoribosylamine-glycine ligase activity Source: EcoCyc

GO - Biological processi

  • 'de novo' IMP biosynthetic process Source: UniProtKB-HAMAP
  • cellular response to DNA damage stimulus Source: EcoliWiki
  • purine nucleobase biosynthetic process Source: InterPro
  • 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.
BRENDAi6.3.4.13. 2026.
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 Componenti: Chromosome UP000000625 Componenti: 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.

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

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
OMAiEPKLENV.
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:
EMBLi
GenBanki
DDBJi
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.

Genome annotation databases

EnsemblBacteriaiAAC76979; AAC76979; b4005.
BAE77314; BAE77314; BAE77314.
GeneIDi948504.
KEGGiecj:Y75_p3191.
eco:b4005.
PATRICi32123535. VBIEscCol129921_4120.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

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

Protein-protein interaction databases

IntActiP15640. 4 interactions.
STRINGi511145.b4005.

2D gel databases

SWISS-2DPAGEP15640.

Proteomic databases

PaxDbiP15640.
PRIDEiP15640.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76979; AAC76979; b4005.
BAE77314; BAE77314; BAE77314.
GeneIDi948504.
KEGGiecj:Y75_p3191.
eco:b4005.
PATRICi32123535. VBIEscCol129921_4120.

Organism-specific databases

EchoBASEiEB0785.
EcoGeneiEG10792. purD.

Phylogenomic databases

eggNOGiCOG0151.
HOGENOMiHOG000033463.
InParanoidiP15640.
KOiK01945.
OMAiEPKLENV.
OrthoDBiEOG69SKD1.
PhylomeDBiP15640.

Enzyme and pathway databases

UniPathwayiUPA00074; UER00125.
BioCyciEcoCyc:GLYCRIBONUCSYN-MONOMER.
ECOL316407:JW3969-MONOMER.
MetaCyc:GLYCRIBONUCSYN-MONOMER.
BRENDAi6.3.4.13. 2026.

Miscellaneous databases

EvolutionaryTraceiP15640.
PROiP15640.

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. "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: June 24, 2015
This is version 139 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

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.