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Protein

Phosphoribosylamine--glycine ligase

Gene

purD

Organism
Streptococcus pyogenes serotype M3 (strain SSI-1)
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 Mg(2+) or Mn2+ ion per subunit.By similarity

Pathway:iIMP 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. no protein annotated in this organism
  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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi284 – 2841Magnesium or manganeseUniRule annotation
Metal bindingi286 – 2861Magnesium or manganeseUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi134 – 19562ATPUniRule annotationAdd
BLAST

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

BioCyciSPYO193567:GHDO-48-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:SPs0027
OrganismiStreptococcus pyogenes serotype M3 (strain SSI-1)
Taxonomic identifieri193567 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeStreptococcus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 421421Phosphoribosylamine--glycine ligasePRO_0000411469Add
BLAST

Structurei

3D structure databases

ProteinModelPortaliP0DD59.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini108 – 314207ATP-graspUniRule annotationAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

HOGENOMiHOG000033463.
KOiK01945.
OrthoDBiEOG69SKD1.

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.
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]
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.

P0DD59-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKLLVVGSGG REHAIAKKLL ASKGVDQVFV APGNDGMTLD GLDLVNIVVS
60 70 80 90 100
EHSRLIAFAK ENEISWAFIG PDDALAAGIV DDFNTAGLRA FGPTKAAAEL
110 120 130 140 150
EWSKDFAKEI MVKYNVPTAA YGTFSDFEKA KAYIEEQGAP IVVKADGLAL
160 170 180 190 200
GKGVVVAETV EQAVEAAQEM LLDNKFGDSG ARVVIEEFLD GEEFSLFAFV
210 220 230 240 250
NGDKFYIMPT AQDHKRAFDG DKGPNTGGMG AYAPVPHLPQ SVVDTAVEMI
260 270 280 290 300
VRPVLEGMVA EGRPYLGVLY VGLILTADGP KVIEFNSRFG DPETQIILPR
310 320 330 340 350
LTSDFAQNID DIMMGIEPYI TWQKDGVTLG VVVASEGYPF DYEKGVPLPE
360 370 380 390 400
KTDGDIITYY AGVKFSENSE LLLSNGGRVY MLVTTEDSVK AGQDKIYTQL
410 420
AQQDPTGLFY RNDIGSKAIR E
Length:421
Mass (Da):45,519
Last modified:July 27, 2011 - v1
Checksum:i469F688FEFB0634B
GO

Sequence cautioni

The sequence BAC63122.1 differs from that shown. Reason: Erroneous initiation. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000034 Genomic DNA. Translation: BAC63122.1. Different initiation.
RefSeqiWP_032461289.1. NC_004606.1.

Genome annotation databases

EnsemblBacteriaiBAC63122; BAC63122; BAC63122.
KEGGisps:SPs0027.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000034 Genomic DNA. Translation: BAC63122.1. Different initiation.
RefSeqiWP_032461289.1. NC_004606.1.

3D structure databases

ProteinModelPortaliP0DD59.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAC63122; BAC63122; BAC63122.
KEGGisps:SPs0027.

Phylogenomic databases

HOGENOMiHOG000033463.
KOiK01945.
OrthoDBiEOG69SKD1.

Enzyme and pathway databases

UniPathwayiUPA00074; UER00125.
BioCyciSPYO193567:GHDO-48-MONOMER.

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.
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]
SUPFAMiSSF51246. SSF51246. 1 hit.
SSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR00877. purD. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
PS00184. GARS. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Genome sequence of an M3 strain of Streptococcus pyogenes reveals a large-scale genomic rearrangement in invasive strains and new insights into phage evolution."
    Nakagawa I., Kurokawa K., Yamashita A., Nakata M., Tomiyasu Y., Okahashi N., Kawabata S., Yamazaki K., Shiba T., Yasunaga T., Hayashi H., Hattori M., Hamada S.
    Genome Res. 13:1042-1055(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: SSI-1.

Entry informationi

Entry nameiPUR2_STRPQ
AccessioniPrimary (citable) accession number: P0DD59
Secondary accession number(s): Q8K8Y4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 27, 2011
Last sequence update: July 27, 2011
Last modified: July 22, 2015
This is version 27 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.