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Protein

Phosphoribosylamine--glycine ligase

Gene

purD

Organism
Yersinia pestis
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

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), 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 bindingi286Magnesium or manganeseUniRule annotation1
Metal bindingi288Magnesium or manganeseUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi135 – 196ATPUniRule annotationAdd BLAST62

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:YPO3729, y0501, YP_3092
OrganismiYersinia pestis
Taxonomic identifieri632 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesYersiniaceaeYersinia
Proteomesi
  • UP000000815 Componenti: Chromosome
  • UP000001019 Componenti: Chromosome
  • UP000002490 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001515061 – 428Phosphoribosylamine--glycine ligaseAdd BLAST428

Proteomic databases

PRIDEiQ8ZAR2.

Interactioni

Protein-protein interaction databases

IntActiQ8ZAR2. 6 interactors.
STRINGi187410.y0501.

Structurei

Secondary structure

1428
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi1 – 7Combined sources7
Helixi10 – 19Combined sources10
Beta strandi25 – 32Combined sources8
Helixi35 – 39Combined sources5
Helixi53 – 62Combined sources10
Beta strandi65 – 70Combined sources6
Helixi73 – 77Combined sources5
Helixi80 – 86Combined sources7
Beta strandi91 – 93Combined sources3
Helixi96 – 103Combined sources8
Helixi105 – 114Combined sources10
Beta strandi122 – 126Combined sources5
Helixi128 – 138Combined sources11
Beta strandi140 – 149Combined sources10
Beta strandi154 – 158Combined sources5
Helixi161 – 172Combined sources12
Helixi175 – 178Combined sources4
Beta strandi184 – 188Combined sources5
Beta strandi192 – 204Combined sources13
Beta strandi206 – 208Combined sources3
Beta strandi212 – 214Combined sources3
Beta strandi217 – 219Combined sources3
Turni220 – 222Combined sources3
Beta strandi223 – 226Combined sources4
Beta strandi230 – 235Combined sources6
Helixi241 – 250Combined sources10
Helixi252 – 261Combined sources10
Beta strandi267 – 276Combined sources10
Beta strandi282 – 287Combined sources6
Helixi289 – 291Combined sources3
Turni293 – 295Combined sources3
Helixi296 – 302Combined sources7
Helixi307 – 315Combined sources9
Helixi319 – 321Combined sources3
Beta strandi331 – 338Combined sources8
Turni339 – 342Combined sources4
Beta strandi362 – 371Combined sources10
Beta strandi377 – 379Combined sources3
Beta strandi381 – 390Combined sources10
Helixi394 – 405Combined sources12
Helixi421 – 424Combined sources4
Turni425 – 427Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3MJFX-ray1.47A1-428[»]
ProteinModelPortaliQ8ZAR2.
SMRiQ8ZAR2.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8ZAR2.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini109 – 316ATP-graspUniRule annotationAdd BLAST208

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105C12. Bacteria.
COG0151. LUCA.
HOGENOMiHOG000033463.
KOiK01945.
OMAiVNGMAAE.

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.

Q8ZAR2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNILIIGNGG REHALGWKAA QSPLADKIYV APGNAGTALE PTLENVDIAA
60 70 80 90 100
TDIAGLLAFA QSHDIGLTIV GPEAPLVIGV VDAFRAAGLA IFGPTQAAAQ
110 120 130 140 150
LEGSKAFTKD FLARHNIPSA EYQNFTDVEA ALAYVRQKGA PIVIKADGLA
160 170 180 190 200
AGKGVIVAMT QEEAETAVND MLAGNAFGDA GHRIVVEEFL DGEEASFIVM
210 220 230 240 250
VDGENVLPMA TSQDHKRVGD GDTGPNTGGM GAYSPAPVVT DDVHQRVMDQ
260 270 280 290 300
VIWPTVRGMA AEGNIYTGFL YAGLMISADG QPKVIEFNCR FGDPETQPIM
310 320 330 340 350
LRMRSDLVEL CLAGTQGKLN EKTSDWDERP SLGVVLAAGG YPADYRQGDV
360 370 380 390 400
IHGLPQQEVK DGKVFHAGTK LNGNHEVVTN GGRVLCVTAL GETVAQAQQY
410 420
AYQLAEGIQW EGVFCRKDIG YRAIARGK
Length:428
Mass (Da):45,317
Last modified:March 27, 2002 - v1
Checksum:i0D12863DD2424EFF
GO

Sequence cautioni

The sequence AAM84090 differs from that shown. Reason: Erroneous initiation.Curated
The sequence AAS63262 differs from that shown. Reason: Erroneous initiation.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL590842 Genomic DNA. Translation: CAL22316.1.
AE009952 Genomic DNA. Translation: AAM84090.1. Different initiation.
AE017042 Genomic DNA. Translation: AAS63262.1. Different initiation.
PIRiAI0453.
RefSeqiWP_002210691.1. NZ_LQBA01000096.1.
YP_002348609.1. NC_003143.1.

Genome annotation databases

EnsemblBacteriaiAAM84090; AAM84090; y0501.
AAS63262; AAS63262; YP_3092.
GeneIDi1176555.
KEGGiype:YPO3729.
ypk:y0501.
ypm:YP_3092.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL590842 Genomic DNA. Translation: CAL22316.1.
AE009952 Genomic DNA. Translation: AAM84090.1. Different initiation.
AE017042 Genomic DNA. Translation: AAS63262.1. Different initiation.
PIRiAI0453.
RefSeqiWP_002210691.1. NZ_LQBA01000096.1.
YP_002348609.1. NC_003143.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3MJFX-ray1.47A1-428[»]
ProteinModelPortaliQ8ZAR2.
SMRiQ8ZAR2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ8ZAR2. 6 interactors.
STRINGi187410.y0501.

Proteomic databases

PRIDEiQ8ZAR2.

Protocols and materials databases

DNASUi1145448.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAM84090; AAM84090; y0501.
AAS63262; AAS63262; YP_3092.
GeneIDi1176555.
KEGGiype:YPO3729.
ypk:y0501.
ypm:YP_3092.

Phylogenomic databases

eggNOGiENOG4105C12. Bacteria.
COG0151. LUCA.
HOGENOMiHOG000033463.
KOiK01945.
OMAiVNGMAAE.

Enzyme and pathway databases

UniPathwayiUPA00074; UER00125.

Miscellaneous databases

EvolutionaryTraceiQ8ZAR2.

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_YERPE
AccessioniPrimary (citable) accession number: Q8ZAR2
Secondary accession number(s): Q0WAS9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 27, 2002
Last sequence update: March 27, 2002
Last modified: November 2, 2016
This is version 113 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.