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Protein

Phosphoribosylamine--glycine ligase

Gene

purD

Organism
Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) (Methanobacterium thermoautotrophicum)
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: 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 bindingi276Magnesium or manganese 1UniRule annotation1
Metal bindingi288Magnesium or manganese 1UniRule annotation1
Metal bindingi288Magnesium or manganese 2UniRule annotation1
Metal bindingi290Magnesium or manganese 2UniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi133 – 196ATPUniRule annotationAdd BLAST64

GO - Molecular functioni

GO - Biological processi

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

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:MTH_1445
OrganismiMethanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) (Methanobacterium thermoautotrophicum)
Taxonomic identifieri187420 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanobacteriaMethanobacterialesMethanobacteriaceaeMethanothermobacter
Proteomesi
  • UP000005223 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001515131 – 436Phosphoribosylamine--glycine ligaseAdd BLAST436

Interactioni

Protein-protein interaction databases

STRINGi187420.MTH1445.

Structurei

3D structure databases

ProteinModelPortaliO27494.
SMRiO27494.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini106 – 318ATP-graspUniRule annotationAdd BLAST213

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi44 – 49Poly-Leu6

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiarCOG04415. Archaea.
COG0151. LUCA.
KOiK01945.
OMAiDEFGPPY.

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. 1 hit.
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]
SMARTiSM01210. GARS_C. 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.

O27494-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKILVVGTGA REHAICSALA DEATIYSVMG NRNPGISRLA GNSLLLLKLT
60 70 80 90 100
PKVVRFASEK GVDMAFIGPE AHLEAGLVDA LEEAGIPSVG PTRDAARIET
110 120 130 140 150
DKSFMRKLFE DYRIPGSITY RVFSDPEELR EFMEDFDSEA VVKPVGLTGG
160 170 180 190 200
KGVKIVGEHL RDNMEALKYA TEVIEKRIGG HPSVVIEERV VGEEFTVQAF
210 220 230 240 250
SDGEHIVPMP AVQDHPHAYE GDQGPITGGM GSYSDSDGLL PFLTQKDYED
260 270 280 290 300
AVEIMQRTVD AIRKETGPYR GILYGQFMLS ADGPKLIEYN ARFGDPEAMN
310 320 330 340 350
VLPLLESSML EICEGIVDGN LKSASFMNLA TVCKYLVPEG YPESGVAGAE
360 370 380 390 400
IKVDEKKIED MGVITYYAAV NQEDDHIYTS SSRALALVAP ADDIYSAEEL
410 420 430
CEEATAHVKG RLYHRRDIGT RELVEKRIKH MEDLRS
Length:436
Mass (Da):47,882
Last modified:May 30, 2000 - v2
Checksum:iDF36C512561D354D
GO

Sequence cautioni

The sequence AAB85920 differs from that shown. Reason: Erroneous initiation.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000666 Genomic DNA. Translation: AAB85920.1. Different initiation.
PIRiD69059.
RefSeqiWP_048061056.1. NC_000916.1.

Genome annotation databases

EnsemblBacteriaiAAB85920; AAB85920; MTH_1445.
GeneIDi1471714.
KEGGimth:MTH_1445.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000666 Genomic DNA. Translation: AAB85920.1. Different initiation.
PIRiD69059.
RefSeqiWP_048061056.1. NC_000916.1.

3D structure databases

ProteinModelPortaliO27494.
SMRiO27494.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi187420.MTH1445.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAB85920; AAB85920; MTH_1445.
GeneIDi1471714.
KEGGimth:MTH_1445.

Phylogenomic databases

eggNOGiarCOG04415. Archaea.
COG0151. LUCA.
KOiK01945.
OMAiDEFGPPY.

Enzyme and pathway databases

UniPathwayiUPA00074; UER00125.

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. 1 hit.
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]
SMARTiSM01210. GARS_C. 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...

Entry informationi

Entry nameiPUR2_METTH
AccessioniPrimary (citable) accession number: O27494
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: May 30, 2000
Last modified: November 2, 2016
This is version 109 of the entry and version 2 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

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 one 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.