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Protein

Phosphoribosylamine--glycine ligase

Gene

purD

Organism
Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
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 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 bindingi134 – 193ATPUniRule annotationAdd BLAST60

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:TK0204
OrganismiThermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
Taxonomic identifieri69014 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaeThermococcus
Proteomesi
  • UP000000536 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001515171 – 431Phosphoribosylamine--glycine ligaseAdd BLAST431

Proteomic databases

PRIDEiQ5JFP1.

Interactioni

Protein-protein interaction databases

STRINGi69014.TK0204.

Structurei

3D structure databases

ProteinModelPortaliQ5JFP1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini107 – 315ATP-graspUniRule annotationAdd BLAST209

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiarCOG04415. Archaea.
COG0151. LUCA.
HOGENOMiHOG000033464.
InParanoidiQ5JFP1.
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.

Q5JFP1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRVLLVGAGG RENAIAEVLA RDAELYVVAG HKNPGIARLA KDYALAKETD
60 70 80 90 100
VPRVLDFALK WGVDMAFIGP EAPLEKGIVN VLEENGVPTV GPTREAAMLE
110 120 130 140 150
TNKAFARWLM EEYKIPGRKL FKVFDDVSEM KSWIDDFGRP VVVKPLGLTG
160 170 180 190 200
GKGVKVVGYQ LKDNEEAKAY AEELIKRDGK VLIEERTDGV EFTFQVFTDG
210 220 230 240 250
KRVVPMPLAQ DYPHAYEGDV GPITGGMGSY SCEDHRLPFI TKEDYEKALE
260 270 280 290 300
TLKATVEAMR KNGTPYKGIL YGQFMLAKDE PKIIEFNARF GDPEAMNVLP
310 320 330 340 350
ILKRSLVEIG EEIVDGNLKG AEFERKATVV KYIAPKGYPT NPVRGIKLHV
360 370 380 390 400
DEAKIREEGA RVYYASLDEN FRMLGSRALA VVGIADSLEE AERIASAGIR
410 420 430
HVRGEIFYRK DVGTRESIAR RIELVRAMRG E
Length:431
Mass (Da):47,925
Last modified:February 15, 2005 - v1
Checksum:iCFFF66298DF5BC37
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP006878 Genomic DNA. Translation: BAD84393.1.
RefSeqiWP_011249159.1. NC_006624.1.

Genome annotation databases

EnsemblBacteriaiBAD84393; BAD84393; TK0204.
GeneIDi3234772.
KEGGitko:TK0204.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP006878 Genomic DNA. Translation: BAD84393.1.
RefSeqiWP_011249159.1. NC_006624.1.

3D structure databases

ProteinModelPortaliQ5JFP1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi69014.TK0204.

Proteomic databases

PRIDEiQ5JFP1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD84393; BAD84393; TK0204.
GeneIDi3234772.
KEGGitko:TK0204.

Phylogenomic databases

eggNOGiarCOG04415. Archaea.
COG0151. LUCA.
HOGENOMiHOG000033464.
InParanoidiQ5JFP1.
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_THEKO
AccessioniPrimary (citable) accession number: Q5JFP1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 30, 2005
Last sequence update: February 15, 2005
Last modified: November 2, 2016
This is version 83 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

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.