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Protein

Phosphoribosylamine--glycine ligase

Gene

purD

Organism
Methanosarcina barkeri (strain Fusaro / DSM 804)
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 bindingi275 – 2751Magnesium or manganese 1UniRule annotation
Metal bindingi287 – 2871Magnesium or manganese 1UniRule annotation
Metal bindingi287 – 2871Magnesium or manganese 2UniRule annotation
Metal bindingi289 – 2891Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi137 – 19458ATPUniRule 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

BioCyciMBAR269797:GHUW-3570-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:Mbar_A3513
OrganismiMethanosarcina barkeri (strain Fusaro / DSM 804)
Taxonomic identifieri269797 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanomicrobiaMethanosarcinalesMethanosarcinaceaeMethanosarcina
ProteomesiUP000008156 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 433433Phosphoribosylamine--glycine ligasePRO_1000018821Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi269797.Mbar_A3513.

Structurei

3D structure databases

ProteinModelPortaliQ465Q9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini110 – 317208ATP-graspUniRule annotationAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0151.
HOGENOMiHOG000033464.
KOiK01945.
OMAiENLECEH.

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.

Q465Q9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKILLIGGGG REHAIAEGIK KSKHNPSLYA LMAKKNPGIA ALCEDFLLEK
60 70 80 90 100
ETEVEKVVEY AKARNIEMAF VGPEAPLAAG VADALWEAGI PVVGPKKSCA
110 120 130 140 150
IIEFDKAWAR NFMKKYGIEG CPEYEVFTEE KPAHDFIEKL GDVAVKPSGL
160 170 180 190 200
TGGKGVKVMG DQLPDLKAAK AYTSELLEKG SVVIEERFIG EEFTLQAFVD
210 220 230 240 250
GKSLVFFPAV QDHKRAYEGD LGPNTGGMGS YTDAGEILPF MLPEDLEKAK
260 270 280 290 300
KIMQDTVKAL SEETGIGYQG ILYGQFILTA SGPKVVEFNA RFGDPEAMNV
310 320 330 340 350
ISLLETDFVD IMSAVVKGTL GNLPVSFSKK ATVCKYAVPA GYPENPEKDS
360 370 380 390 400
EVTVEDIGDA SIYYASVYEK EGKVYTTSSR AIAVIGIAET IAAAEKIAQN
410 420 430
ALENLHGKLF FRKDIGTAAL IQKRIDHMKE LRG
Length:433
Mass (Da):46,905
Last modified:September 13, 2005 - v1
Checksum:iFE1CFE41937107CC
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000099 Genomic DNA. Translation: AAZ72383.1.
RefSeqiWP_011308422.1. NC_007355.1.
YP_306963.1. NC_007355.1.

Genome annotation databases

EnsemblBacteriaiAAZ72383; AAZ72383; Mbar_A3513.
GeneIDi3625401.
KEGGimba:Mbar_A3513.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000099 Genomic DNA. Translation: AAZ72383.1.
RefSeqiWP_011308422.1. NC_007355.1.
YP_306963.1. NC_007355.1.

3D structure databases

ProteinModelPortaliQ465Q9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi269797.Mbar_A3513.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAZ72383; AAZ72383; Mbar_A3513.
GeneIDi3625401.
KEGGimba:Mbar_A3513.

Phylogenomic databases

eggNOGiCOG0151.
HOGENOMiHOG000033464.
KOiK01945.
OMAiENLECEH.

Enzyme and pathway databases

UniPathwayiUPA00074; UER00125.
BioCyciMBAR269797:GHUW-3570-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. "The Methanosarcina barkeri genome: comparative analysis with Methanosarcina acetivorans and Methanosarcina mazei reveals extensive rearrangement within methanosarcinal genomes."
    Maeder D.L., Anderson I., Brettin T.S., Bruce D.C., Gilna P., Han C.S., Lapidus A., Metcalf W.W., Saunders E., Tapia R., Sowers K.R.
    J. Bacteriol. 188:7922-7931(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Fusaro / DSM 804.

Entry informationi

Entry nameiPUR2_METBF
AccessioniPrimary (citable) accession number: Q465Q9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: September 13, 2005
Last modified: May 27, 2015
This is version 83 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, Reference 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.