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Protein

Phosphoribosylamine--glycine ligase

Gene

purD

Organism
Agrobacterium fabrum (strain C58 / ATCC 33970) (Agrobacterium tumefaciens (strain C58))
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 1 Mg2+ or Mn2+ ion 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 bindingi282Magnesium or manganeseUniRule annotation1
Metal bindingi284Magnesium or manganeseUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi133 – 193ATPUniRule annotationAdd BLAST61

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:Atu0647
ORF Names:AGR_C_1152
OrganismiAgrobacterium fabrum (strain C58 / ATCC 33970) (Agrobacterium tumefaciens (strain C58))
Taxonomic identifieri176299 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesRhizobiaceaeRhizobium/Agrobacterium groupAgrobacteriumAgrobacterium tumefaciens complex
Proteomesi
  • UP000000813 Componenti: Chromosome circular

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001514321 – 423Phosphoribosylamine--glycine ligaseAdd BLAST423

Interactioni

Protein-protein interaction databases

STRINGi176299.Atu0647.

Structurei

3D structure databases

ProteinModelPortaliQ8UHN3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini107 – 312ATP-graspUniRule annotationAdd BLAST206

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105C12. Bacteria.
COG0151. LUCA.
HOGENOMiHOG000033463.
KOiK01945.
OMAiFGSAQDH.

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.

Q8UHN3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKVLLIGSGG REHALAWKIA QSPLIDALYA APGNPGIADH ATLVSLDVED
60 70 80 90 100
HAAVIAFAKE KAIDFVVIGP EAPLVAGLAD DLRAAGIATF GPSKAAAQLE
110 120 130 140 150
GSKGFTKDLC ARYDIPTGAY ERFKAAEPAK DYVRAQGAPI VIKADGLAAG
160 170 180 190 200
KGVTVAMTEA EALAAIDDCF DGAFGTAGTE VVVEAFLDGE EASFFCLSDG
210 220 230 240 250
KTALALATAQ DHKRVGDGDT GPNTGGMGAY SPAPVMTPAM VERTMKEIIE
260 270 280 290 300
PTISGMAKDG NPFSGVFFAG LMITAKGPEL IEYNVRFGDP ECQVLMMRLK
310 320 330 340 350
SDLLPILYAT ATGTLDKVQA EWRDDAALTV VLASKGYPGA YDKNTPIAHI
360 370 380 390 400
PEASEEAKVF HAGTALKDGK LVATGGRVLN VTAFGRNVTE AQARAYALAD
410 420
KVEWENGFCR RDIGWQAIAR EKA
Length:423
Mass (Da):44,339
Last modified:November 15, 2002 - v2
Checksum:i33A78649486772B8
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE007869 Genomic DNA. Translation: AAK86455.2.
PIRiAI2655.
F97437.
RefSeqiNP_353670.2. NC_003062.2.
WP_010971036.1. NC_003062.2.

Genome annotation databases

EnsemblBacteriaiAAK86455; AAK86455; Atu0647.
GeneIDi1132685.
KEGGiatu:Atu0647.
PATRICi20810993. VBIAgrTum91616_0640.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE007869 Genomic DNA. Translation: AAK86455.2.
PIRiAI2655.
F97437.
RefSeqiNP_353670.2. NC_003062.2.
WP_010971036.1. NC_003062.2.

3D structure databases

ProteinModelPortaliQ8UHN3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi176299.Atu0647.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAK86455; AAK86455; Atu0647.
GeneIDi1132685.
KEGGiatu:Atu0647.
PATRICi20810993. VBIAgrTum91616_0640.

Phylogenomic databases

eggNOGiENOG4105C12. Bacteria.
COG0151. LUCA.
HOGENOMiHOG000033463.
KOiK01945.
OMAiFGSAQDH.

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_AGRFC
AccessioniPrimary (citable) accession number: Q8UHN3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 15, 2002
Last sequence update: November 15, 2002
Last modified: November 2, 2016
This is version 90 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.