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Protein

Phosphoribosylamine--glycine ligase

Gene

purD

Organism
Phenylobacterium zucineum (strain HLK1)
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 bindingi270Magnesium or manganese 1UniRule annotation1
Metal bindingi282Magnesium or manganese 1UniRule annotation1
Metal bindingi282Magnesium or manganese 2UniRule annotation1
Metal bindingi284Magnesium or manganese 2UniRule 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:PHZ_c0508
OrganismiPhenylobacterium zucineum (strain HLK1)
Taxonomic identifieri450851 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaCaulobacteralesCaulobacteraceaePhenylobacterium
Proteomesi
  • UP000001868 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000960351 – 423Phosphoribosylamine--glycine ligaseAdd BLAST423

Interactioni

Protein-protein interaction databases

STRINGi450851.PHZ_c0508.

Structurei

3D structure databases

ProteinModelPortaliB4REI0.
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.
OrthoDBiPOG091H02DZ.

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.

B4REI0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNILLVGSGG REHALAWKIA ASPLVKRLVA APGNPGMAEQ CELRAVGPTD
60 70 80 90 100
VPALVALAKE IAADLVVIGP ESSVDAGLAD QLQAEGIPCF GPTAGAGQLE
110 120 130 140 150
SSKAFTKAFA DRYGLPTAAY RVCESAEAAR AALELFEPPY VIKADGLAAG
160 170 180 190 200
KGVTVAQDRG EAEAAIDDAF GGRFGAAGAR VVVEEFLEGE IGSLFALCDG
210 220 230 240 250
EASMLFGWAQ DHKRVFDGEQ GPNTGGMGTY SPAPVFTPEL VEQVRTRLVE
260 270 280 290 300
PAFAGIAADG SPYRGVLFVE LMATKHGPKL VEFNVRFGDP ECQVLMLRLE
310 320 330 340 350
SDLVPYLVAC ANGTLGDMPP PVWRDEAAVC VVIAAKGYPG TPAAGGEIRG
360 370 380 390 400
LDQDLGDDVV VFHAGTKRDA DGTLRAAGGR VLNVCARGAD LRTARDRAYA
410 420
AIERIEFADG FCRSDIGWRA LGR
Length:423
Mass (Da):44,229
Last modified:September 23, 2008 - v1
Checksum:iCAD06E9B49DA13FB
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000747 Genomic DNA. Translation: ACG76922.1.
RefSeqiWP_012521070.1. NC_011144.1.

Genome annotation databases

EnsemblBacteriaiACG76922; ACG76922; PHZ_c0508.
KEGGipzu:PHZ_c0508.
PATRICi22923628. VBIPheZuc44517_0908.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000747 Genomic DNA. Translation: ACG76922.1.
RefSeqiWP_012521070.1. NC_011144.1.

3D structure databases

ProteinModelPortaliB4REI0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi450851.PHZ_c0508.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACG76922; ACG76922; PHZ_c0508.
KEGGipzu:PHZ_c0508.
PATRICi22923628. VBIPheZuc44517_0908.

Phylogenomic databases

eggNOGiENOG4105C12. Bacteria.
COG0151. LUCA.
HOGENOMiHOG000033463.
KOiK01945.
OMAiFGSAQDH.
OrthoDBiPOG091H02DZ.

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_PHEZH
AccessioniPrimary (citable) accession number: B4REI0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: September 23, 2008
Last modified: November 2, 2016
This is version 50 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.