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Protein

Phosphoribosylamine--glycine ligase

Gene

purD

Organism
Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (strain Fiocruz L1-130)
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)
  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 bindingi290 – 2901Magnesium or manganeseUniRule annotation
Metal bindingi292 – 2921Magnesium or manganeseUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi139 – 20062ATPUniRule 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

BioCyciLINT267671:GHQI-471-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:LIC_10472
OrganismiLeptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (strain Fiocruz L1-130)
Taxonomic identifieri267671 [NCBI]
Taxonomic lineageiBacteriaSpirochaetesLeptospiralesLeptospiraceaeLeptospira
ProteomesiUP000007037 Componenti: Chromosome I

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 426426Phosphoribosylamine--glycine ligasePRO_0000151458Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi267671.LIC10472.

Structurei

3D structure databases

ProteinModelPortaliQ72V31.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini113 – 320208ATP-graspUniRule annotationAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

KOiK01945.
OMAiENLECEH.
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.

Q72V31-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQVKLKVLLI GSGGRESAIA FYLRKSVLLS ELKVFPGNGG FPDQELLPPD
60 70 80 90 100
SFQVLDKNSV QSFLKQNPFD LIVVGPEDPL VAGFADWAAE LNIPVFGPDS
110 120 130 140 150
FCAQVEGSKD FAKSLMTEAK IPTAEYKTFS EYSDSLKYLE SKSIPIVIKA
160 170 180 190 200
DGLAAGKGVT VATSKEMAQT ALKEIFKDKK FGSSGNQVVI EEFMEGQEAS
210 220 230 240 250
IFAISDGDSY FLLPAAQDHK RAFDGDQGPN TGGMGAYCPA PVISESILQK
260 270 280 290 300
VKEQIFDPMF DLFRKKGHPY RGLLYAGLMI SPNGEPKVVE FNCRFGDPET
310 320 330 340 350
QCVLAMLDGD LLELLYRAST GKIKGIQAAV KKGAAVVVVL AAQGYPDFYE
360 370 380 390 400
KNIPLNLPET SGQNVHLFHA GTLKKDGKVF SSGGRILGIV AQGADLKSSV
410 420
DQAYSFLEKI QAPKTFYRKD IGYRAL
Length:426
Mass (Da):46,258
Last modified:July 5, 2004 - v1
Checksum:iD0F4ABC2A9349E68
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016823 Genomic DNA. Translation: AAS69093.1.
RefSeqiWP_001197373.1. NC_005823.1.
YP_000456.1. NC_005823.1.

Genome annotation databases

EnsemblBacteriaiAAS69093; AAS69093; LIC_10472.
KEGGilic:LIC10472.
PATRICi22372768. VBILepInt6257_0558.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016823 Genomic DNA. Translation: AAS69093.1.
RefSeqiWP_001197373.1. NC_005823.1.
YP_000456.1. NC_005823.1.

3D structure databases

ProteinModelPortaliQ72V31.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi267671.LIC10472.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAS69093; AAS69093; LIC_10472.
KEGGilic:LIC10472.
PATRICi22372768. VBILepInt6257_0558.

Phylogenomic databases

KOiK01945.
OMAiENLECEH.
OrthoDBiEOG69SKD1.

Enzyme and pathway databases

UniPathwayiUPA00074; UER00125.
BioCyciLINT267671:GHQI-471-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. "Comparative genomics of two Leptospira interrogans serovars reveals novel insights into physiology and pathogenesis."
    Nascimento A.L.T.O., Ko A.I., Martins E.A.L., Monteiro-Vitorello C.B., Ho P.L., Haake D.A., Verjovski-Almeida S., Hartskeerl R.A., Marques M.V., Oliveira M.C., Menck C.F.M., Leite L.C.C., Carrer H., Coutinho L.L., Degrave W.M., Dellagostin O.A., El-Dorry H., Ferro E.S.
    , Ferro M.I.T., Furlan L.R., Gamberini M., Giglioti E.A., Goes-Neto A., Goldman G.H., Goldman M.H.S., Harakava R., Jeronimo S.M.B., Junqueira-de-Azevedo I.L.M., Kimura E.T., Kuramae E.E., Lemos E.G.M., Lemos M.V.F., Marino C.L., Nunes L.R., de Oliveira R.C., Pereira G.G., Reis M.S., Schriefer A., Siqueira W.J., Sommer P., Tsai S.M., Simpson A.J.G., Ferro J.A., Camargo L.E.A., Kitajima J.P., Setubal J.C., Van Sluys M.A.
    J. Bacteriol. 186:2164-2172(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Fiocruz L1-130.

Entry informationi

Entry nameiPUR2_LEPIC
AccessioniPrimary (citable) accession number: Q72V31
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 15, 2005
Last sequence update: July 5, 2004
Last modified: June 24, 2015
This is version 79 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. 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.