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Protein

Phosphoribosylamine--glycine ligase

Gene

purD

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

Functioni

Catalytic activityi

ATP + 5-phospho-D-ribosylamine + glycine = ADP + phosphate + N1-(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

BioCyciVPAR223926:G1GTB-3016-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: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

Proteomic databases

PRIDEiQ87KS8

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
OMAiKATVCKY

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_sf
IPR020561 PRibGlycinamid_synth_ATP-grasp
IPR000115 PRibGlycinamide_synth
IPR020560 PRibGlycinamide_synth_C-dom
IPR037123 PRibGlycinamide_synth_C_sf
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
PATRICifig|223926.6.peg.2788

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 23, 2018
This is version 97 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

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