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Protein

Phosphoribosylamine--glycine ligase

Gene

purD

Organism
Aquifex aeolicus (strain VF5)
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)
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 bindingi283Magnesium or manganeseUniRule annotation1
Metal bindingi285Magnesium or manganeseUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi133 – 194ATPUniRule 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

BRENDAi6.3.4.13. 396.
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:aq_742
OrganismiAquifex aeolicus (strain VF5)
Taxonomic identifieri224324 [NCBI]
Taxonomic lineageiBacteriaAquificaeAquificalesAquificaceaeAquifex
Proteomesi
  • UP000000798 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001514341 – 424Phosphoribosylamine--glycine ligaseAdd BLAST424

Interactioni

Protein-protein interaction databases

STRINGi224324.aq_742.

Structurei

Secondary structure

1424
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 9Combined sources8
Helixi10 – 19Combined sources10
Beta strandi26 – 32Combined sources7
Helixi37 – 39Combined sources3
Beta strandi41 – 44Combined sources4
Helixi51 – 61Combined sources11
Beta strandi64 – 68Combined sources5
Helixi71 – 75Combined sources5
Helixi78 – 84Combined sources7
Beta strandi89 – 91Combined sources3
Turni94 – 97Combined sources4
Helixi98 – 101Combined sources4
Helixi103 – 112Combined sources10
Beta strandi120 – 124Combined sources5
Helixi126 – 136Combined sources11
Beta strandi138 – 146Combined sources9
Beta strandi152 – 158Combined sources7
Helixi159 – 170Combined sources12
Helixi176 – 179Combined sources4
Beta strandi180 – 186Combined sources7
Beta strandi190 – 200Combined sources11
Beta strandi203 – 206Combined sources4
Beta strandi210 – 212Combined sources3
Beta strandi215 – 217Combined sources3
Turni218 – 220Combined sources3
Beta strandi221 – 224Combined sources4
Beta strandi228 – 233Combined sources6
Helixi239 – 248Combined sources10
Helixi250 – 260Combined sources11
Beta strandi265 – 275Combined sources11
Beta strandi278 – 287Combined sources10
Turni290 – 292Combined sources3
Helixi293 – 298Combined sources6
Helixi304 – 312Combined sources9
Beta strandi323 – 332Combined sources10
Turni334 – 337Combined sources4
Helixi349 – 353Combined sources5
Beta strandi358 – 368Combined sources11
Beta strandi371 – 374Combined sources4
Beta strandi376 – 388Combined sources13
Helixi389 – 400Combined sources12
Turni414 – 418Combined sources5
Helixi419 – 421Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2YW2X-ray1.80A/B1-424[»]
2YYAX-ray2.40A/B1-424[»]
ProteinModelPortaliO66949.
SMRiO66949.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO66949.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini107 – 313ATP-graspUniRule annotationAdd BLAST207

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4107QNG. Bacteria.
COG0151. LUCA.
HOGENOMiHOG000033463.
InParanoidiO66949.
KOiK01945.
OMAiVNGMAAE.
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.

O66949-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKVLVVGNGG REHAIAWKVA QSPLVKELYV AKGNAGIWEI AKRVDISPTD
60 70 80 90 100
VEKLAEFAKN EGVDFTIVGP EAPLVEGIVD EFEKRGLKIF GPNKEAAKLE
110 120 130 140 150
GSKAFAKTFM KKYGIPTARY EVFTDFEKAK EYVEKVGAPI VVKADGLAAG
160 170 180 190 200
KGAVVCETVE KAIETLDRFL NKKIFGKSSE RVVIEEFLEG EEASYIVMIN
210 220 230 240 250
GDRYVPLPTS QDHKRLLDED KGPNTGGMGA YSPTPVINEE VEKRIREEIV
260 270 280 290 300
ERVIKGLKEE GIYYRGFLYA GLMITKEGPK VLEFNVRLGD PEAQPILMRV
310 320 330 340 350
KNDFLETLLN FYEGKDVHIK EDERYALDVV LASRGYPEKP ETGKIIHGLD
360 370 380 390 400
YLKSMEDVVV FHAGTKKEGN FTVTSGGRVL NVCAYGKTLK EAKERAYEAI
410 420
RYVCFEGMHY RKDIGDKAFK YLSE
Length:424
Mass (Da):47,430
Last modified:August 1, 1998 - v1
Checksum:i06EB10D23A68E2FD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000657 Genomic DNA. Translation: AAC06907.1.
PIRiB70365.
RefSeqiNP_213510.1. NC_000918.1.
WP_010880448.1. NC_000918.1.

Genome annotation databases

EnsemblBacteriaiAAC06907; AAC06907; aq_742.
GeneIDi1193399.
KEGGiaae:aq_742.
PATRICi20958924. VBIAquAeo85532_0593.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000657 Genomic DNA. Translation: AAC06907.1.
PIRiB70365.
RefSeqiNP_213510.1. NC_000918.1.
WP_010880448.1. NC_000918.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2YW2X-ray1.80A/B1-424[»]
2YYAX-ray2.40A/B1-424[»]
ProteinModelPortaliO66949.
SMRiO66949.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224324.aq_742.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC06907; AAC06907; aq_742.
GeneIDi1193399.
KEGGiaae:aq_742.
PATRICi20958924. VBIAquAeo85532_0593.

Phylogenomic databases

eggNOGiENOG4107QNG. Bacteria.
COG0151. LUCA.
HOGENOMiHOG000033463.
InParanoidiO66949.
KOiK01945.
OMAiVNGMAAE.
OrthoDBiPOG091H02DZ.

Enzyme and pathway databases

UniPathwayiUPA00074; UER00125.
BRENDAi6.3.4.13. 396.

Miscellaneous databases

EvolutionaryTraceiO66949.

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_AQUAE
AccessioniPrimary (citable) accession number: O66949
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: August 1, 1998
Last modified: November 2, 2016
This is version 110 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.