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Protein

Phosphoribosylamine--glycine ligase

Gene

purD

Organism
Methanosphaera stadtmanae (strain ATCC 43021 / DSM 3091 / JCM 11832 / MCB-3)
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 bindingi277Magnesium or manganese 1UniRule annotation1
Metal bindingi289Magnesium or manganese 1UniRule annotation1
Metal bindingi289Magnesium or manganese 2UniRule annotation1
Metal bindingi291Magnesium or manganese 2UniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi134 – 197ATPUniRule annotationAdd BLAST64

GO - Molecular functioni

GO - Biological processi

Keywordsi

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

Enzyme and pathway databases

UniPathwayi
UPA00074;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:Msp_0030
OrganismiMethanosphaera stadtmanae (strain ATCC 43021 / DSM 3091 / JCM 11832 / MCB-3)
Taxonomic identifieri339860 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanomada groupMethanobacteriaMethanobacterialesMethanobacteriaceaeMethanosphaera
Proteomesi
  • UP000001931 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000188291 – 438Phosphoribosylamine--glycine ligaseAdd BLAST438

Interactioni

Protein-protein interaction databases

STRINGi339860.Msp_0030

Structurei

3D structure databases

ProteinModelPortaliQ2NI86
SMRiQ2NI86
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini107 – 319ATP-graspUniRule annotationAdd BLAST213

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.

Q2NI86-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKILMVGSGA REHAIAKALN KTADVYTYMG RKNPGLARIS KNYTVNDESN
60 70 80 90 100
FNEIIKFAQE NNVELAFIGP EAPLEMGIVD ELEKEGIHSV GPTKSAAQIE
110 120 130 140 150
TNKAFMRKLF EDYDIPGSIK YGTFYDLDEA YEFIDNFDEP VVVKPIGLTG
160 170 180 190 200
GKGVKIVGDQ LADNDEAKEY VKEIFHQKMG GFEGVVIEEL LLGEEYTIQA
210 220 230 240 250
FVDGTHLIPM PAAQDHPHAF VGNKGPITGG MGSYSDKNHL LPFLTQEDYD
260 270 280 290 300
KSVEIMEKTI KAIAKEQEPY KGILYGQFML CKDGPKVIEY NARFGDPESM
310 320 330 340 350
NVLSVIDDDL AKISKQIVDG TLDSVNFLNK SSVCKYVVPD KYPNTHVADT
360 370 380 390 400
VVDVDEDKIN ELGAQVFYAA VYQDMDDSIK LTSSRALGVL AVKDSIKEAE
410 420 430
KICEEAIKYV KGEVYHRNDV ATEELLNEKI KHMEEVRL
Length:438
Mass (Da):48,794
Last modified:February 7, 2006 - v1
Checksum:iC59F9094D2DA0186
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000102 Genomic DNA Translation: ABC56449.1
RefSeqiWP_011405648.1, NC_007681.1

Genome annotation databases

EnsemblBacteriaiABC56449; ABC56449; Msp_0030
GeneIDi3855038
KEGGimst:Msp_0030

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000102 Genomic DNA Translation: ABC56449.1
RefSeqiWP_011405648.1, NC_007681.1

3D structure databases

ProteinModelPortaliQ2NI86
SMRiQ2NI86
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi339860.Msp_0030

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABC56449; ABC56449; Msp_0030
GeneIDi3855038
KEGGimst:Msp_0030

Phylogenomic databases

eggNOGiarCOG04415 Archaea
COG0151 LUCA
HOGENOMiHOG000033464
KOiK01945
OMAiKATVCKY
OrthoDBiPOG093Z02WG

Enzyme and pathway databases

UniPathwayi
UPA00074;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_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
ProtoNetiSearch...

Entry informationi

Entry nameiPUR2_METST
AccessioniPrimary (citable) accession number: Q2NI86
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: February 7, 2006
Last modified: October 10, 2018
This is version 84 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. SIMILARITY comments
    Index of protein domains and families
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
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Main funding by: National Institutes of Health

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