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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: -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 bindingi134 – 193ATPUniRule annotationAdd BLAST60

GO - Molecular functioni

GO - Biological processi

Keywordsi

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

Enzyme and pathway databases

BioCyciTKOD69014:G1G2A-202-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: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
SMRiQ5JFP1
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

Phylogenomic databases

eggNOGiarCOG04415 Archaea
COG0151 LUCA
HOGENOMiHOG000033464
InParanoidiQ5JFP1
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.

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
PATRICifig|69014.16.peg.203

Similar proteinsi

Entry informationi

Entry nameiPUR2_THEKO
AccessioniPrimary (citable) accession number: Q5JFP1
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 30, 2005
Last sequence update: February 15, 2005
Last modified: February 28, 2018
This is version 91 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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