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Protein

Phosphoribosylamine--glycine ligase

Gene

purD

Organism
Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
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 bindingi273Magnesium or manganeseUniRule annotation1
Metal bindingi275Magnesium or manganeseUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi133 – 184ATPUniRule annotationAdd BLAST52

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:SCO4068
ORF Names:SCD25.04
OrganismiStreptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
Taxonomic identifieri100226 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaStreptomycetalesStreptomycetaceaeStreptomycesStreptomyces albidoflavus group
Proteomesi
  • UP000001973 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001514861 – 416Phosphoribosylamine--glycine ligaseAdd BLAST416

Proteomic databases

PRIDEiQ9RKL4.

Interactioni

Protein-protein interaction databases

STRINGi100226.SCO4068.

Structurei

3D structure databases

ProteinModelPortaliQ9RKL4.
SMRiQ9RKL4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini107 – 303ATP-graspUniRule annotationAdd BLAST197

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105C12. Bacteria.
COG0151. LUCA.
HOGENOMiHOG000033463.
InParanoidiQ9RKL4.
KOiK01945.
OMAiFGSAQDH.
OrthoDBiPOG091H02DZ.
PhylomeDBiQ9RKL4.

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.

Q9RKL4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKVLVIGGGA REHALCRSLS LDPDVTALHC APGNAGIAEV AELHQVDALD
60 70 80 90 100
GAAVTALAGR LGAELVVVGP EAPLVAGVAD AVREAGIPVF GPSGEAARLE
110 120 130 140 150
GSKAFAKDVM ACAGVPTARS YVCTNPAEVD AALAAFGAPY VVKDDGLAAG
160 170 180 190 200
KGVVVTDDVE AARAHANACD RVVVEEFLDG PEVSLFAVTD GENVRPLQPA
210 220 230 240 250
QDFKRALDGD EGPNTGGMGA YSPLPWADPK LVDEVVQSVL QPTVDEMRRR
260 270 280 290 300
GTPFSGLLYA GLAITSRGVR VIEFNARFGD PETQVVLARL KTPLAGLLMA
310 320 330 340 350
AATGNLADLE PLRWSDEAAV TVVVASHNYP GTPRTGDPIT GLDEVAAQDA
360 370 380 390 400
PHAYVLHAGT RAEGDAVVSA GGRVLSVTAT GADLTEARDR AYRAVARIGL
410
DGSQHRTDIA AKAAGA
Length:416
Mass (Da):42,623
Last modified:May 1, 2000 - v1
Checksum:i21715503DEEF70B3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL939118 Genomic DNA. Translation: CAB56348.1.
RefSeqiNP_628249.1. NC_003888.3.
WP_011029417.1. NC_003888.3.

Genome annotation databases

EnsemblBacteriaiCAB56348; CAB56348; CAB56348.
GeneIDi1099505.
KEGGisco:SCO4068.
PATRICi23737902. VBIStrCoe124346_4127.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL939118 Genomic DNA. Translation: CAB56348.1.
RefSeqiNP_628249.1. NC_003888.3.
WP_011029417.1. NC_003888.3.

3D structure databases

ProteinModelPortaliQ9RKL4.
SMRiQ9RKL4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi100226.SCO4068.

Proteomic databases

PRIDEiQ9RKL4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB56348; CAB56348; CAB56348.
GeneIDi1099505.
KEGGisco:SCO4068.
PATRICi23737902. VBIStrCoe124346_4127.

Phylogenomic databases

eggNOGiENOG4105C12. Bacteria.
COG0151. LUCA.
HOGENOMiHOG000033463.
InParanoidiQ9RKL4.
KOiK01945.
OMAiFGSAQDH.
OrthoDBiPOG091H02DZ.
PhylomeDBiQ9RKL4.

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_STRCO
AccessioniPrimary (citable) accession number: Q9RKL4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 15, 2002
Last sequence update: May 1, 2000
Last modified: November 2, 2016
This is version 97 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.