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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: 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 2 magnesium or manganese ions per subunit.By similarity

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi277 – 2771Magnesium or manganese 1UniRule annotation
Metal bindingi289 – 2891Magnesium or manganese 1UniRule annotation
Metal bindingi289 – 2891Magnesium or manganese 2UniRule annotation
Metal bindingi291 – 2911Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi134 – 19764ATPUniRule annotationAdd
BLAST

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-HAMAP
  2. magnesium ion binding Source: UniProtKB-HAMAP
  3. manganese ion binding Source: UniProtKB-HAMAP
  4. phosphoribosylamine-glycine ligase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. 'de novo' IMP biosynthetic process Source: UniProtKB-HAMAP
  2. purine nucleobase biosynthetic process Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Purine biosynthesis

Keywords - Ligandi

ATP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciMSTA339860:GJEZ-30-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:Msp_0030
OrganismiMethanosphaera stadtmanae (strain ATCC 43021 / DSM 3091 / JCM 11832 / MCB-3)
Taxonomic identifieri339860 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanobacteriaMethanobacterialesMethanobacteriaceaeMethanosphaera
ProteomesiUP000001931: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 438438Phosphoribosylamine--glycine ligasePRO_1000018829Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi339860.Msp_0030.

Structurei

3D structure databases

ProteinModelPortaliQ2NI86.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini107 – 319213ATP-graspUniRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the GARS family.UniRule annotation
Contains 1 ATP-grasp domain.UniRule annotation

Phylogenomic databases

eggNOGiCOG0151.
HOGENOMiHOG000033464.
KOiK01945.
OMAiENLECEH.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
3.40.50.20. 1 hit.
3.90.600.10. 1 hit.
HAMAPiMF_00138. GARS.
InterProiIPR011761. ATP-grasp.
IPR013815. ATP_grasp_subdomain_1.
IPR013816. ATP_grasp_subdomain_2.
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.
[Graphical view]
PfamiPF01071. GARS_A. 1 hit.
PF02843. GARS_C. 1 hit.
PF02844. GARS_N. 1 hit.
[Graphical view]
SUPFAMiSSF51246. SSF51246. 1 hit.
SSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR00877. purD. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
PS00184. GARS. 1 hit.
[Graphical view]

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.
YP_447092.1. NC_007681.1.

Genome annotation databases

EnsemblBacteriaiABC56449; ABC56449; Msp_0030.
GeneIDi3855038.
KEGGimst:Msp_0030.

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.
YP_447092.1. NC_007681.1.

3D structure databases

ProteinModelPortaliQ2NI86.
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

eggNOGiCOG0151.
HOGENOMiHOG000033464.
KOiK01945.
OMAiENLECEH.

Enzyme and pathway databases

UniPathwayiUPA00074; UER00125.
BioCyciMSTA339860:GJEZ-30-MONOMER.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
3.40.50.20. 1 hit.
3.90.600.10. 1 hit.
HAMAPiMF_00138. GARS.
InterProiIPR011761. ATP-grasp.
IPR013815. ATP_grasp_subdomain_1.
IPR013816. ATP_grasp_subdomain_2.
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.
[Graphical view]
PfamiPF01071. GARS_A. 1 hit.
PF02843. GARS_C. 1 hit.
PF02844. GARS_N. 1 hit.
[Graphical view]
SUPFAMiSSF51246. SSF51246. 1 hit.
SSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR00877. purD. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
PS00184. GARS. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis."
    Fricke W.F., Seedorf H., Henne A., Kruer M., Liesegang H., Hedderich R., Gottschalk G., Thauer R.K.
    J. Bacteriol. 188:642-658(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 43021 / DSM 3091 / JCM 11832 / MCB-3.

Entry informationi

Entry nameiPUR2_METST
AccessioniPrimary (citable) accession number: Q2NI86
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: February 7, 2006
Last modified: February 4, 2015
This is version 69 of the entry and version 1 of the sequence. [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

External Data

Dasty 3

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 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.