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Protein

Phosphoribosylamine--glycine ligase

Gene

purD

Organism
Bacillus subtilis (strain 168)
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

BioCyciBSUB:BSU06530-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:BSU06530
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001514361 – 422Phosphoribosylamine--glycine ligaseAdd BLAST422

Proteomic databases

PaxDbiP12039.

Interactioni

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100003688.

Structurei

Secondary structure

1422
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 7Combined sources6
Helixi10 – 19Combined sources10
Beta strandi26 – 32Combined sources7
Helixi35 – 37Combined sources3
Turni38 – 40Combined sources3
Helixi51 – 60Combined sources10
Beta strandi63 – 68Combined sources6
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
Helixi148 – 150Combined sources3
Beta strandi153 – 158Combined sources6
Helixi159 – 170Combined sources12
Helixi176 – 179Combined sources4
Beta strandi180 – 186Combined sources7
Beta strandi190 – 200Combined sources11
Beta strandi203 – 206Combined sources4
Beta strandi210 – 217Combined sources8
Helixi218 – 220Combined sources3
Beta strandi221 – 233Combined sources13
Helixi239 – 248Combined sources10
Helixi250 – 259Combined sources10
Beta strandi265 – 275Combined sources11
Beta strandi278 – 287Combined sources10
Turni290 – 292Combined sources3
Helixi293 – 296Combined sources4
Helixi297 – 299Combined sources3
Helixi304 – 312Combined sources9
Beta strandi325 – 333Combined sources9
Turni334 – 337Combined sources4
Beta strandi345 – 347Combined sources3
Beta strandi353 – 365Combined sources13
Beta strandi367 – 372Combined sources6
Beta strandi374 – 386Combined sources13
Helixi387 – 401Combined sources15
Helixi414 – 420Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2XCLX-ray2.10A1-422[»]
2XD4X-ray2.65A1-422[»]
ProteinModelPortaliP12039.
SMRiP12039.
ModBaseiSearch...
MobiDBiSearch...

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

eggNOGiENOG4105C12. Bacteria.
COG0151. LUCA.
HOGENOMiHOG000033463.
InParanoidiP12039.
KOiK01945.
OMAiFGSAQDH.
PhylomeDBiP12039.

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.

P12039-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNVLIIGKGG REHTLAWKAA QSSLVENVFA APGNDGMAAS AQLVNIEESD
60 70 80 90 100
HAGLVSFAKQ NQVGLTIVGP EVPLIEGLVD EFEKAGLHVF GPSKAAAIIE
110 120 130 140 150
GSKQFAKDLM KKYDIPTAEY ETFTSFDEAK AYVQEKGAPI VIKADGLAAG
160 170 180 190 200
KGVTVAMTEE EAIACLHDFL EDEKFGDASA SVVIEEYLSG EEFSLMAFVK
210 220 230 240 250
GEKVYPMVIA QDHKRAFDGD KGPNTGGMGA YSPVPQISEE TVRHAVETIV
260 270 280 290 300
KPAAKAMVQE GRSFTGVLYA GLMLTENGSK VIEFNARFGD PETQVVLPRM
310 320 330 340 350
ESDLVQVLLD LLDDKEVDLR WKDTAAVSVV LASEGYPESY AKGTPIGSLA
360 370 380 390 400
AETEQVVVFH AGTKAEGGEF VTNGGRVANV TAFDETFEAA RDRVYKAVDE
410 420
IFKPGLFFRK DIGARALKAA QK
Length:422
Mass (Da):45,280
Last modified:October 1, 1989 - v1
Checksum:i4EF390A85CC90FB2
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J02732 Genomic DNA. Translation: AAA22684.1.
AF011544 Genomic DNA. Translation: AAB72186.1.
AL009126 Genomic DNA. Translation: CAB12473.1.
PIRiB29183. AJBSAG.
RefSeqiNP_388535.1. NC_000964.3.
WP_003242993.1. NZ_JNCM01000032.1.

Genome annotation databases

EnsemblBacteriaiCAB12473; CAB12473; BSU06530.
GeneIDi938741.
KEGGibsu:BSU06530.
PATRICi18972948. VBIBacSub10457_0688.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J02732 Genomic DNA. Translation: AAA22684.1.
AF011544 Genomic DNA. Translation: AAB72186.1.
AL009126 Genomic DNA. Translation: CAB12473.1.
PIRiB29183. AJBSAG.
RefSeqiNP_388535.1. NC_000964.3.
WP_003242993.1. NZ_JNCM01000032.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2XCLX-ray2.10A1-422[»]
2XD4X-ray2.65A1-422[»]
ProteinModelPortaliP12039.
SMRiP12039.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100003688.

Proteomic databases

PaxDbiP12039.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB12473; CAB12473; BSU06530.
GeneIDi938741.
KEGGibsu:BSU06530.
PATRICi18972948. VBIBacSub10457_0688.

Phylogenomic databases

eggNOGiENOG4105C12. Bacteria.
COG0151. LUCA.
HOGENOMiHOG000033463.
InParanoidiP12039.
KOiK01945.
OMAiFGSAQDH.
PhylomeDBiP12039.

Enzyme and pathway databases

UniPathwayiUPA00074; UER00125.
BioCyciBSUB:BSU06530-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. 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_BACSU
AccessioniPrimary (citable) accession number: P12039
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1989
Last sequence update: October 1, 1989
Last modified: November 2, 2016
This is version 127 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. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.