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Protein

Phosphoribosylamine--glycine ligase

Gene

purD

Organism
Methanococcus maripaludis (strain C5 / ATCC BAA-1333)
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 2 magnesium or manganese ions 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 bindingi282 – 2821Magnesium or manganese 1UniRule annotation
Metal bindingi294 – 2941Magnesium or manganese 1UniRule annotation
Metal bindingi294 – 2941Magnesium or manganese 2UniRule annotation
Metal bindingi296 – 2961Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi140 – 20263ATPUniRule 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

BioCyciMMAR402880:GJ2R-1261-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:MmarC5_1246
OrganismiMethanococcus maripaludis (strain C5 / ATCC BAA-1333)
Taxonomic identifieri402880 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanococciMethanococcalesMethanococcaceaeMethanococcus
ProteomesiUP000000253 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 444444Phosphoribosylamine--glycine ligasePRO_1000018824Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi402880.MmarC5_1246.

Structurei

3D structure databases

ProteinModelPortaliA4FZB0.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini109 – 324216ATP-graspUniRule annotationAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0151.
HOGENOMiHOG000033464.
KOiK01945.
OMAiGPELIEY.

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.

A4FZB0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKVLLIGGGA REHAIAMALK KNELVELYTL MKNKNPGIYA ISDEVSFNSE
60 70 80 90 100
TDVPAIKEFA EKIKPELAVI GPEAPLGVGA ADLLIEMGIP TVGPKKLPAQ
110 120 130 140 150
IETSKEFMRN LFKKYEIDGS LRYAAFNEYG NDLETFIDEM TSLGKDVVVK
160 170 180 190 200
PAGLTGGKGV KVVGEQLKDN EEAKIYAKEV FDKSIGGGNI IIEEKLVGVE
210 220 230 240 250
FTLHGFVDGE NIVFMPAVQD HPHAYNNDEG PITGGMGSYS CPNHGLPFLS
260 270 280 290 300
AEMLDRAEKI MEKTVSSINS EVGPYNGFLY GQFMLTADGP KIIEYNARFG
310 320 330 340 350
DPEAMNLLPI LKTDFLDVCF AIAEGKLDKI NLEFENKATV CKYVVPNGYP
360 370 380 390 400
IDPVRNKELT VDEKAIENAD AILFYASINE KNGKLYITGS RSAAVVGISE
410 420 430 440
NIEEAEKIAQ MAIENFKGEV YYRSDIGTLG LIKKRIERVK QLAK
Length:444
Mass (Da):48,696
Last modified:April 17, 2007 - v1
Checksum:iB61CAD4435796E34
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000609 Genomic DNA. Translation: ABO35544.1.
RefSeqiWP_011868997.1. NC_009135.1.
YP_001097758.1. NC_009135.1.

Genome annotation databases

EnsemblBacteriaiABO35544; ABO35544; MmarC5_1246.
GeneIDi4929077.
KEGGimmq:MmarC5_1246.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000609 Genomic DNA. Translation: ABO35544.1.
RefSeqiWP_011868997.1. NC_009135.1.
YP_001097758.1. NC_009135.1.

3D structure databases

ProteinModelPortaliA4FZB0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi402880.MmarC5_1246.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABO35544; ABO35544; MmarC5_1246.
GeneIDi4929077.
KEGGimmq:MmarC5_1246.

Phylogenomic databases

eggNOGiCOG0151.
HOGENOMiHOG000033464.
KOiK01945.
OMAiGPELIEY.

Enzyme and pathway databases

UniPathwayiUPA00074; UER00125.
BioCyciMMAR402880:GJ2R-1261-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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C5 / ATCC BAA-1333.

Entry informationi

Entry nameiPUR2_METM5
AccessioniPrimary (citable) accession number: A4FZB0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: April 17, 2007
Last modified: April 1, 2015
This is version 55 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.