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Protein

Phosphoribosylamine--glycine ligase

Gene

purD

Organism
Methanoculleus marisnigri (strain ATCC 35101 / DSM 1498 / JR1)
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 bindingi273Magnesium or manganese 1UniRule annotation1
Metal bindingi285Magnesium or manganese 1UniRule annotation1
Metal bindingi285Magnesium or manganese 2UniRule annotation1
Metal bindingi287Magnesium or manganese 2UniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi138 – 193ATPUniRule annotationAdd BLAST56

GO - Molecular functioni

GO - Biological processi

Keywordsi

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

Enzyme and pathway databases

BioCyciMMAR368407:G1G85-1003-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:Memar_1000
OrganismiMethanoculleus marisnigri (strain ATCC 35101 / DSM 1498 / JR1)
Taxonomic identifieri368407 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanomicrobiaMethanomicrobialesMethanomicrobiaceaeMethanoculleus
Proteomesi
  • UP000002146 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000188261 – 430Phosphoribosylamine--glycine ligaseAdd BLAST430

Proteomic databases

PRIDEiA3CU83

Interactioni

Protein-protein interaction databases

STRINGi368407.Memar_1000

Structurei

3D structure databases

ProteinModelPortaliA3CU83
SMRiA3CU83
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini111 – 315ATP-graspUniRule annotationAdd BLAST205

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.

A3CU83-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDMKVLVVGG GGREHAITRA LSCNSDTKIF SVMARKNPGI ARLSERVLLE
60 70 80 90 100
KETNIEKVIP FATNCGVDAA VIGPEAPLEA GIVDRLEAAG IPSLGPTRAA
110 120 130 140 150
ARIETDKAFC RRLMERHGIA GCPEYRVCRD PEEARRFIES YDGDLAVKPI
160 170 180 190 200
GLTGGKGVRI MGEHVDVAGA VEYAREIGGS VVLEERLVGE EFTLQAFVDG
210 220 230 240 250
EHLIPMPLVQ DHKRAYEGDV GPNTGGMGSY SLADHMLPFV SRRDYEKALR
260 270 280 290 300
IMTDTVAAMR AEGTPYRGIL YGQFMNTREG PKVIEFNARF GDPEAMNVLS
310 320 330 340 350
LLESDFAGIV GHIIEGDLAP SHVRFAKKAT VCKYLVPEGY PDAPRANEPL
360 370 380 390 400
TLGDYGDALL YYASVEERDG TLHTLTSRTL AFVGRGETLE EAEAIAEKAA
410 420 430
SSVSGSVFHR RDIGTPEILE KRCQHMREIL
Length:430
Mass (Da):46,875
Last modified:March 20, 2007 - v1
Checksum:iEF618C6B8DAE8F24
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000562 Genomic DNA Translation: ABN56933.1
RefSeqiWP_011843844.1, NC_009051.1

Genome annotation databases

EnsemblBacteriaiABN56933; ABN56933; Memar_1000
GeneIDi4847274
KEGGimem:Memar_1000

Similar proteinsi

Entry informationi

Entry nameiPUR2_METMJ
AccessioniPrimary (citable) accession number: A3CU83
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: March 20, 2007
Last modified: May 23, 2018
This is version 70 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

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