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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 Mg2+ or Mn2+ ion per subunit.By similarity

Pathwayi: 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)
  2. 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)DescriptionActionsGraphical viewLength
Metal bindingi286Magnesium or manganeseBy similarity1
Metal bindingi288Magnesium or manganeseBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi135 – 196ATPBy similarityAdd BLAST62

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10792. purD.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001514481 – 429Phosphoribosylamine--glycine ligaseAdd BLAST429

Proteomic databases

PaxDbiP15640.
PRIDEiP15640.

2D gel databases

SWISS-2DPAGEP15640.

Interactioni

Subunit structurei

Monomer.

Protein-protein interaction databases

BioGridi4262462. 10 interactors.
IntActiP15640. 4 interactors.
STRINGi511145.b4005.

Structurei

Secondary structure

1429
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi1 – 7Combined sources7
Helixi10 – 19Combined sources10
Beta strandi25 – 32Combined sources8
Helixi35 – 39Combined sources5
Beta strandi43 – 45Combined sources3
Helixi53 – 62Combined sources10
Beta strandi66 – 70Combined sources5
Helixi73 – 77Combined sources5
Helixi80 – 86Combined sources7
Beta strandi91 – 93Combined sources3
Turni96 – 99Combined sources4
Helixi100 – 103Combined sources4
Helixi105 – 114Combined sources10
Beta strandi122 – 129Combined sources8
Helixi130 – 138Combined sources9
Beta strandi140 – 145Combined sources6
Beta strandi155 – 160Combined sources6
Helixi161 – 168Combined sources8
Turni169 – 172Combined sources4
Beta strandi184 – 188Combined sources5
Beta strandi192 – 204Combined sources13
Beta strandi206 – 219Combined sources14
Turni220 – 222Combined sources3
Beta strandi223 – 235Combined sources13
Helixi241 – 250Combined sources10
Helixi252 – 261Combined sources10
Beta strandi267 – 277Combined sources11
Beta strandi282 – 290Combined sources9
Turni293 – 295Combined sources3
Helixi296 – 302Combined sources7
Helixi307 – 315Combined sources9
Helixi319 – 321Combined sources3
Beta strandi328 – 338Combined sources11
Turni339 – 342Combined sources4
Beta strandi362 – 371Combined sources10
Beta strandi377 – 379Combined sources3
Beta strandi381 – 393Combined sources13
Helixi394 – 404Combined sources11
Turni405 – 407Combined sources3
Helixi421 – 425Combined sources5

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP15640.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini109 – 316ATP-graspAdd BLAST208

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105C12. Bacteria.
COG0151. LUCA.
HOGENOMiHOG000033463.
InParanoidiP15640.
KOiK01945.
OMAiVNGMAAE.
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. 1 hit.
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]
SMARTiSM01210. GARS_C. 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)DescriptionActionsGraphical viewLength
Sequence conflicti15 – 16LA → WR in AAA24455 (PubMed:2687276).Curated2
Sequence conflicti97G → V in AAA24455 (PubMed:2687276).Curated1

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.
WP_000866800.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76979; AAC76979; b4005.
BAE77314; BAE77314; BAE77314.
GeneIDi948504.
KEGGiecj:JW3969.
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.
WP_000866800.1. NZ_LN832404.1.

3D structure databases

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

Protein-protein interaction databases

BioGridi4262462. 10 interactors.
IntActiP15640. 4 interactors.
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:JW3969.
eco:b4005.
PATRICi32123535. VBIEscCol129921_4120.

Organism-specific databases

EchoBASEiEB0785.
EcoGeneiEG10792. purD.

Phylogenomic databases

eggNOGiENOG4105C12. Bacteria.
COG0151. LUCA.
HOGENOMiHOG000033463.
InParanoidiP15640.
KOiK01945.
OMAiVNGMAAE.
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. 1 hit.
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]
SMARTiSM01210. GARS_C. 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...

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: November 2, 2016
This is version 146 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

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 one 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.