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Protein

Phosphoribosylamine--glycine ligase

Gene

purD

Organism
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
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), 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 bindingi273Magnesium or manganeseUniRule annotation1
Metal bindingi275Magnesium or manganeseUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi125 – 186ATPUniRule 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

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:TM_1250
OrganismiThermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Taxonomic identifieri243274 [NCBI]
Taxonomic lineageiBacteriaThermotogaeThermotogalesThermotogaceaeThermotoga
Proteomesi
  • UP000008183 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001514951 – 400Phosphoribosylamine--glycine ligaseAdd BLAST400

Interactioni

Protein-protein interaction databases

STRINGi243274.TM1250.

Structurei

Secondary structure

1400
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi5 – 10Combined sources6
Helixi13 – 24Combined sources12
Beta strandi28 – 33Combined sources6
Helixi38 – 40Combined sources3
Beta strandi42 – 44Combined sources3
Helixi50 – 54Combined sources5
Helixi67 – 69Combined sources3
Beta strandi81 – 83Combined sources3
Helixi86 – 93Combined sources8
Helixi95 – 104Combined sources10
Beta strandi112 – 117Combined sources6
Helixi118 – 125Combined sources8
Beta strandi130 – 138Combined sources9
Beta strandi145 – 150Combined sources6
Helixi151 – 162Combined sources12
Beta strandi165 – 167Combined sources3
Beta strandi174 – 178Combined sources5
Beta strandi182 – 192Combined sources11
Beta strandi195 – 198Combined sources4
Beta strandi207 – 209Combined sources3
Turni210 – 212Combined sources3
Beta strandi213 – 216Combined sources4
Beta strandi220 – 224Combined sources5
Helixi230 – 249Combined sources20
Beta strandi255 – 265Combined sources11
Beta strandi268 – 277Combined sources10
Helixi282 – 289Combined sources8
Helixi291 – 303Combined sources13
Beta strandi314 – 322Combined sources9
Turni324 – 328Combined sources5
Beta strandi344 – 352Combined sources9
Beta strandi355 – 358Combined sources4
Beta strandi360 – 372Combined sources13
Helixi373 – 386Combined sources14

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1VKZX-ray2.30A/B1-400[»]
ProteinModelPortaliQ9X0X7.
SMRiQ9X0X7.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9X0X7.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini99 – 303ATP-graspUniRule annotationAdd BLAST205

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4107QNG. Bacteria.
COG0151. LUCA.
InParanoidiQ9X0X7.
KOiK01945.
OMAiDEFGPPY.

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.

Q9X0X7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKAVRVHILG SGGREHAIGW AFAKQGYEVH FYPGNAGTKR DGTNHPYEGE
60 70 80 90 100
KTLKAIPEED IVIPGSEEFL VEGVSNWRSN VFGPVKEVAR LEGSKVYAKR
110 120 130 140 150
FMKKYGIRTA RFEVAETPEE LREKIKKFSP PYVIKADGLA RGKGVLILDS
160 170 180 190 200
KEETIEKGSK LIIGELIKGV KGPVVIDEFL AGNELSAMAV VNGRNFVILP
210 220 230 240 250
FVRDYKRLMD GDRGPNTGGM GSWGPVEIPS DTIKKIEELF DKTLWGVEKE
260 270 280 290 300
GYAYRGFLYL GLMLHDGDPY ILEYNVRLGD PETEVIVTLN PEGFVNAVLE
310 320 330 340 350
GYRGGKMEPV EPRGFAVDVV LAARGYPDAP EKGKEITLPE EGLIFFAGVA
360 370 380 390 400
EKDGKLVTNG GRVLHCMGTG ETKEEARRKA YELAEKVHFE GKTYRRDIAL
Length:400
Mass (Da):44,326
Last modified:November 1, 1999 - v1
Checksum:i411CE014DD7DE90F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000512 Genomic DNA. Translation: AAD36325.1.
PIRiD72277.
RefSeqiNP_229055.1. NC_000853.1.
WP_010865290.1. NC_000853.1.

Genome annotation databases

EnsemblBacteriaiAAD36325; AAD36325; TM_1250.
GeneIDi898233.
KEGGitma:TM1250.
tmi:THEMA_08085.
PATRICi23937440. VBITheMar51294_1266.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000512 Genomic DNA. Translation: AAD36325.1.
PIRiD72277.
RefSeqiNP_229055.1. NC_000853.1.
WP_010865290.1. NC_000853.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1VKZX-ray2.30A/B1-400[»]
ProteinModelPortaliQ9X0X7.
SMRiQ9X0X7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243274.TM1250.

Protocols and materials databases

DNASUi898233.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAD36325; AAD36325; TM_1250.
GeneIDi898233.
KEGGitma:TM1250.
tmi:THEMA_08085.
PATRICi23937440. VBITheMar51294_1266.

Phylogenomic databases

eggNOGiENOG4107QNG. Bacteria.
COG0151. LUCA.
InParanoidiQ9X0X7.
KOiK01945.
OMAiDEFGPPY.

Enzyme and pathway databases

UniPathwayiUPA00074; UER00125.

Miscellaneous databases

EvolutionaryTraceiQ9X0X7.

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_THEMA
AccessioniPrimary (citable) accession number: Q9X0X7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: November 1, 1999
Last modified: November 30, 2016
This is version 120 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. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.