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Protein

Phosphoribosylamine--glycine ligase

Gene

purD

Organism
Methanococcoides burtonii (strain DSM 6242 / NBRC 107633 / OCM 468 / ACE-M)
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 2 magnesium or manganese ions 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 bindingi274Magnesium or manganese 1UniRule annotation1
Metal bindingi286Magnesium or manganese 1UniRule annotation1
Metal bindingi286Magnesium or manganese 2UniRule annotation1
Metal bindingi288Magnesium or manganese 2UniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi137 – 194ATPUniRule annotationAdd BLAST58

GO - Molecular functioni

GO - Biological processi

Keywordsi

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

Enzyme and pathway databases

BioCyciMBUR259564:G1G6A-1105-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:Mbur_1056
OrganismiMethanococcoides burtonii (strain DSM 6242 / NBRC 107633 / OCM 468 / ACE-M)
Taxonomic identifieri259564 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanomicrobiaMethanosarcinalesMethanosarcinaceaeMethanococcoides
Proteomesi
  • UP000001979 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000188221 – 432Phosphoribosylamine--glycine ligaseAdd BLAST432

Proteomic databases

PRIDEiQ12X37

Interactioni

Protein-protein interaction databases

STRINGi259564.Mbur_1056

Structurei

3D structure databases

ProteinModelPortaliQ12X37
SMRiQ12X37
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini110 – 316ATP-graspUniRule annotationAdd BLAST207

Sequence similaritiesi

Belongs to the GARS family.UniRule annotation

Phylogenomic databases

eggNOGiarCOG04415 Archaea
COG0151 LUCA
HOGENOMiHOG000033464
KOiK01945
OMAiKATVCKY
OrthoDBiPOG093Z02WG

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.

Q12X37-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNVLIIGGGG RENAIADAIA RSERNPALFA VMAKKNPGIA ALCEDFLLAK
60 70 80 90 100
ETDVEKVVGY AREKGIEMVF IGPEAPLAVG LADALEDAGI GAVGPRKNVA
110 120 130 140 150
RIEFDKAWAR NFMKDNDIEG SPAFKVFSDK EGLQEYIEEL GSVAIKPAGL
160 170 180 190 200
TGGKGVKVMG DQLPDTGAAY DYAVSLLDGD NVVVEENLVG EEFTVQAFVD
210 220 230 240 250
GKNLAFTPCV QDHKRAFEND FGPNTGGMGS YSDSDGLLPF VTIDDLYHAR
260 270 280 290 300
EIMKATITAL GATETPFKGM LYGQFILTKN GPKVIEFNAR FGDPEAMNVL
310 320 330 340 350
PLLKTDMIDV MSAVVNGTLD ELDVEFLKRA TVCKYAVPAG YPDEPSKDKE
360 370 380 390 400
VVVGNIGDAL LFYSSVYEKD GKVYTTSSRA VAVVGVANSI TDAEVIAQNA
410 420 430
LENITGDLHF RRDIGTPELV QRRVTHMEQI RR
Length:432
Mass (Da):46,602
Last modified:August 22, 2006 - v1
Checksum:iF1387CED0A63839E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000300 Genomic DNA Translation: ABE51989.1
RefSeqiWP_011499138.1, NC_007955.1

Genome annotation databases

EnsemblBacteriaiABE51989; ABE51989; Mbur_1056
GeneIDi3998796
KEGGimbu:Mbur_1056

Similar proteinsi

Entry informationi

Entry nameiPUR2_METBU
AccessioniPrimary (citable) accession number: Q12X37
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: August 22, 2006
Last modified: May 23, 2018
This is version 79 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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