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Protein

Phosphoribosylamine--glycine ligase

Gene

purD

Organism
Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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 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.UniRule annotation
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 manganeseUniRule annotation1
Metal bindingi288Magnesium or manganeseUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi135 – 196ATPUniRule annotationAdd BLAST62

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionLigase
Biological processPurine biosynthesis
LigandATP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

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:VP2898
OrganismiVibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
Taxonomic identifieri223926 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
Proteomesi
  • UP000002493 Componenti: Chromosome 1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001514981 – 429Phosphoribosylamine--glycine ligaseAdd BLAST429

Interactioni

Protein-protein interaction databases

STRINGi223926.VP2898.

Structurei

3D structure databases

ProteinModelPortaliQ87KS8.
SMRiQ87KS8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

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

Sequence similaritiesi

Belongs to the GARS family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105C12. Bacteria.
COG0151. LUCA.
HOGENOMiHOG000033463.
KOiK01945.
OMAiVNGMAAE.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.90.600.10. 1 hit.
HAMAPiMF_00138. GARS. 1 hit.
InterProiView protein in InterPro
IPR011761. ATP-grasp.
IPR013815. ATP_grasp_subdomain_1.
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.
PfamiView protein in Pfam
PF01071. GARS_A. 1 hit.
PF02843. GARS_C. 1 hit.
PF02844. GARS_N. 1 hit.
SMARTiView protein in SMART
SM01210. GARS_C. 1 hit.
SUPFAMiSSF51246. SSF51246. 1 hit.
SSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR00877. purD. 1 hit.
PROSITEiView protein in PROSITE
PS50975. ATP_GRASP. 1 hit.
PS00184. GARS. 1 hit.

Sequencei

Sequence statusi: Complete.

Q87KS8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRVLIIGSGG REHALGWKAA QNPNVETIFI APGNAGTALE PKLENVNIDV
60 70 80 90 100
EDIAGLVAFA KEKAIELTIV GPEAPLVIGV VDAFREAGLP IFGPTQAAAQ
110 120 130 140 150
LEGSKAFTKD FLARHQIPTG AYANFTEIEP ALAYVREQGA PIVVKADGLA
160 170 180 190 200
AGKGVIVAMT LEEAEDAIKD MLAGNAFGDA GSRVVIEEFL DGEEASFIVM
210 220 230 240 250
VDGENVLPMA TSQDHKRVGD KDTGPNTGGM GAYSPAPVVT PEIHNRIMEE
260 270 280 290 300
VIYPTVRGMA SEGNPYTGFL YAGLMIDKDG TPKVIEYNCR FGDPETQPIM
310 320 330 340 350
MRMESDLVDL CLAAIDEKLD QVESKWDPRA SIGIVLAAGG YPAAYNKGDV
360 370 380 390 400
ISGLPQVEIE GEKVFHAGTD NQDGDIVTNG GRVLCATALG NSVSEAQQRA
410 420
YELAKQISWD GMFHRNDIGY RAIAREQEK
Length:429
Mass (Da):45,791
Last modified:May 23, 2003 - v1
Checksum:i03124D4773881E5E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000031 Genomic DNA. Translation: BAC61161.1.
RefSeqiNP_799277.1. NC_004603.1.
WP_005456447.1. NC_004603.1.

Genome annotation databases

EnsemblBacteriaiBAC61161; BAC61161; BAC61161.
GeneIDi1190473.
KEGGivpa:VP2898.
PATRICi20144042. VBIVibPar50997_2788.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000031 Genomic DNA. Translation: BAC61161.1.
RefSeqiNP_799277.1. NC_004603.1.
WP_005456447.1. NC_004603.1.

3D structure databases

ProteinModelPortaliQ87KS8.
SMRiQ87KS8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi223926.VP2898.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAC61161; BAC61161; BAC61161.
GeneIDi1190473.
KEGGivpa:VP2898.
PATRICi20144042. VBIVibPar50997_2788.

Phylogenomic databases

eggNOGiENOG4105C12. Bacteria.
COG0151. LUCA.
HOGENOMiHOG000033463.
KOiK01945.
OMAiVNGMAAE.

Enzyme and pathway databases

UniPathwayiUPA00074; UER00125.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.90.600.10. 1 hit.
HAMAPiMF_00138. GARS. 1 hit.
InterProiView protein in InterPro
IPR011761. ATP-grasp.
IPR013815. ATP_grasp_subdomain_1.
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.
PfamiView protein in Pfam
PF01071. GARS_A. 1 hit.
PF02843. GARS_C. 1 hit.
PF02844. GARS_N. 1 hit.
SMARTiView protein in SMART
SM01210. GARS_C. 1 hit.
SUPFAMiSSF51246. SSF51246. 1 hit.
SSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR00877. purD. 1 hit.
PROSITEiView protein in PROSITE
PS50975. ATP_GRASP. 1 hit.
PS00184. GARS. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiPUR2_VIBPA
AccessioniPrimary (citable) accession number: Q87KS8
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 23, 2003
Last sequence update: May 23, 2003
Last modified: May 10, 2017
This is version 92 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. 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.