Q5JFP1 (PUR2_PYRKO) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Phosphoribosylamine--glycine ligase
EC=6.3.4.13

Alternative name(s):
GARS
Glycinamide ribonucleotide synthetase
Phosphoribosylglycinamide synthetase

Gene names

Name:	purD
Ordered Locus Names:	TK0204

Organism

Pyrococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Thermococcus kodakaraensis (strain KOD1))

Taxonomic identifier

69014 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Thermococcus

Protein attributes

Sequence length	431 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

General annotation (Comments)

Catalytic activity	ATP + 5-phospho-D-ribosylamine + glycine = ADP + phosphate + N(1)-(5-phospho-D-ribosyl)glycinamide. HAMAP MF_00138
Cofactor	Binds 2 magnesium or manganese ions per subunit By similarity.
Pathway	Purine metabolism; IMP biosynthesis via de novo pathway; N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-alpha-D-ribose 1-diphosphate: step 2/2. HAMAP MF_00138
Sequence similarities	Belongs to the GARS family. Contains 1 ATP-grasp domain.

Ontologies

Keywords
Biological process	Purine biosynthesis
Ligand	ATP-binding Magnesium Manganese Metal-binding Nucleotide-binding
Molecular function	Ligase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	purine base biosynthetic process Inferred from electronic annotation. Source: InterPro purine nucleotide biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW phosphoribosylamine-glycine ligase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 431	431	Phosphoribosylamine--glycine ligase HAMAP MF_00138		PRO_0000151517
Regions
	Domain	107 – 315	209	ATP-grasp
	Nucleotide binding	134 – 193	60	ATP By similarity
Sites
	Metal binding	273	1	Magnesium or manganese 1 By similarity
	Metal binding	285	1	Magnesium or manganese 1 By similarity
	Metal binding	285	1	Magnesium or manganese 2 By similarity
	Metal binding	287	1	Magnesium or manganese 2 By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q5JFP1 [UniParc]. Last modified February 15, 2005. Version 1. Checksum: CFFF66298DF5BC37	FASTA	431	47,925
	10 20 30 40 50 60 MRVLLVGAGG RENAIAEVLA RDAELYVVAG HKNPGIARLA KDYALAKETD VPRVLDFALK 70 80 90 100 110 120 WGVDMAFIGP EAPLEKGIVN VLEENGVPTV GPTREAAMLE TNKAFARWLM EEYKIPGRKL 130 140 150 160 170 180 FKVFDDVSEM KSWIDDFGRP VVVKPLGLTG GKGVKVVGYQ LKDNEEAKAY AEELIKRDGK 190 200 210 220 230 240 VLIEERTDGV EFTFQVFTDG KRVVPMPLAQ DYPHAYEGDV GPITGGMGSY SCEDHRLPFI 250 260 270 280 290 300 TKEDYEKALE TLKATVEAMR KNGTPYKGIL YGQFMLAKDE PKIIEFNARF GDPEAMNVLP 310 320 330 340 350 360 ILKRSLVEIG EEIVDGNLKG AEFERKATVV KYIAPKGYPT NPVRGIKLHV DEAKIREEGA 370 380 390 400 410 420 RVYYASLDEN FRMLGSRALA VVGIADSLEE AERIASAGIR HVRGEIFYRK DVGTRESIAR 430 RIELVRAMRG E

References

[1]

"Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes." Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T. Genome Res. 15:352-363(2005) [PubMed: 15710748] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC BAA-918 / JCM 12380 / KOD1.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AP006878 Genomic DNA. Translation: BAD84393.1.
RefSeq	YP_182617.1. NC_006624.1.
3D structure databases
ProteinModelPortal	Q5JFP1.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	EBPYRT00000006782; EBPYRP00000006563; EBPYRG00000006781.
GeneID	3234772.
GenomeReviews	Gene locus TK0204 in contig AP006878_GR.
KEGG	tko:TK0204.
NMPDR	fig|69014.3.peg.459.
Phylogenomic databases
eggNOG	arNOG04186.
GeneTree	EBGT00050000022712.
HOGENOM	HBG404060.
OMA	MGAYTPL.
PhylomeDB	Q5JFP1.
ProtClustDB	PRK00885.
Enzyme and pathway databases
BioCyc	TKOD69014:TK0204-MONOMER.
Family and domain databases
HAMAP	MF_00138. GARS. [Tree]
InterPro	IPR011761. ATP-grasp. IPR013815. ATP_grasp_subdomain_1. IPR013816. ATP_grasp_subdomain_2. IPR013817. Pre-ATP_grasp. IPR016185. PreATP-grasp-like. 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]
Gene3D	G3DSA:3.30.1490.20. ATP_grasp_subdomain_1. 1 hit. G3DSA:3.30.470.20. ATP_grasp_subdomain_2. 1 hit. G3DSA:3.90.600.10. Gars. 1 hit. G3DSA:3.40.50.20. Pre-ATP_grasp. 1 hit.
KO	K01945.
Pfam	PF01071. GARS_A. 1 hit. PF02843. GARS_C. 1 hit. PF02844. GARS_N. 1 hit. [Graphical view]
SUPFAM	SSF52440. PreATP-grasp-like. 1 hit. SSF51246. Rudmnt_hyb_motif. 1 hit.
TIGRFAMs	TIGR00877. PurD. 1 hit.
PROSITE	PS50975. ATP_GRASP. 1 hit. PS00184. GARS. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

PUR2_PYRKO

Accession

Primary (citable) accession number: Q5JFP1

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 30, 2005
Last sequence update:	February 15, 2005
Last modified:	December 14, 2011
This is version 56 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program