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Protein

Phosphoribosylamine--glycine ligase

Gene

purD

Organism
Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094)
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: 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), 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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi282 – 2821Magnesium or manganeseUniRule annotation
Metal bindingi284 – 2841Magnesium or manganeseUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi133 – 19361ATPUniRule 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

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:BMEI1519
OrganismiBrucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094)
Taxonomic identifieri224914 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBrucellaceaeBrucella
ProteomesiUP000000419 Componenti: Chromosome I

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 427427Phosphoribosylamine--glycine ligasePRO_0000151437Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi224914.BAWG_0706.

Structurei

3D structure databases

ProteinModelPortaliQ8YFK1.
SMRiQ8YFK1. Positions 1-422.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini107 – 312206ATP-graspUniRule annotationAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

HOGENOMiHOG000033463.
KOiK01945.
OMAiGPELIEY.
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.

Q8YFK1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKVLLIGSGG REHALAWKLA ASPLLEKLYC ALGNPGIAAV AELADIGVDD
60 70 80 90 100
HAALIAFAKE KHIDLVVVGP EAPLVAGLAD EMRAEGIRVF GPSRAAAQLE
110 120 130 140 150
GSKGFTKDLC ARFNIPTGAY GRFNNAPKAK AYIRQQGAPI VVKADGLAAG
160 170 180 190 200
KGVVVAMTLQ EALDAVDSCF EGAFGAAGAE VVVEEFLDGE EASFFCICDG
210 220 230 240 250
KTALPLGSAQ DHKRVGDGDT GPNTGGMGAY APAPVMTPEM VARTMRELIE
260 270 280 290 300
PTMRGMAEIG APFSGILFAG LMITSDGPKL IEYNTRFGDP ECQVLMMRLN
310 320 330 340 350
SDLLALVNAA VDGRLDEVSL EWKDEPALTV VMAAEGYPAN VKKGSVIRDL
360 370 380 390 400
EKLESIDGVK LFHAGTALKD GAIVASGGRV LNITATAATV AQAQARAYEA
410 420
LKLIDWPEGF YRSDIGWRAV EREKANR
Length:427
Mass (Da):44,973
Last modified:March 27, 2002 - v1
Checksum:iC4ADF63267DD5826
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE008917 Genomic DNA. Translation: AAL52700.1.
PIRiAI3441.
RefSeqiNP_540436.1. NC_003317.1.
WP_004686770.1. NZ_GG703778.1.

Genome annotation databases

EnsemblBacteriaiAAL52700; AAL52700; BMEI1519.
KEGGibme:BMEI1519.
PATRICi17796919. VBIBruMel146950_0279.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE008917 Genomic DNA. Translation: AAL52700.1.
PIRiAI3441.
RefSeqiNP_540436.1. NC_003317.1.
WP_004686770.1. NZ_GG703778.1.

3D structure databases

ProteinModelPortaliQ8YFK1.
SMRiQ8YFK1. Positions 1-422.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224914.BAWG_0706.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL52700; AAL52700; BMEI1519.
KEGGibme:BMEI1519.
PATRICi17796919. VBIBruMel146950_0279.

Phylogenomic databases

HOGENOMiHOG000033463.
KOiK01945.
OMAiGPELIEY.
OrthoDBiEOG69SKD1.

Enzyme and pathway databases

UniPathwayiUPA00074; UER00125.

Miscellaneous databases

PROiQ8YFK1.

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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 16M / ATCC 23456 / NCTC 10094.

Entry informationi

Entry nameiPUR2_BRUME
AccessioniPrimary (citable) accession number: Q8YFK1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 27, 2002
Last sequence update: March 27, 2002
Last modified: June 24, 2015
This is version 86 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

Documents

  1. Brucella melitensis
    Brucella melitensis (strain 16M): entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. 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.