P15640 (PUR2_ECOLI) 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:	b4005, JW3969

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	429 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Catalytic activity	ATP + 5-phospho-D-ribosylamine + glycine = ADP + phosphate + N(1)-(5-phospho-D-ribosyl)glycinamide. HAMAP-Rule MF_00138
Cofactor	Binds 1 magnesium or manganese ion 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-Rule MF_00138
Subunit structure	Monomer.
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	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	'de novo' IMP biosynthetic process Inferred from electronic annotation. Source: UniProtKB-UniPathway purine nucleobase biosynthetic process Inferred from electronic annotation. Source: InterPro purine nucleotide biosynthetic process Non-traceable author statement Ref.2. Source: EcoliWiki response to DNA damage stimulus Inferred from expression pattern PubMed 11967071. Source: EcoliWiki
Molecular_function	ATP binding Inferred from direct assay Ref.2. Source: EcoliWiki ATPase activity, coupled Inferred from direct assay Ref.2. Source: EcoliWiki magnesium ion binding Inferred from electronic annotation. Source: HAMAP manganese ion binding Inferred from electronic annotation. Source: HAMAP phosphoribosylamine-glycine ligase activity Inferred from direct assay Ref.2. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 429

429

Phosphoribosylamine--glycine ligase HAMAP-Rule MF_00138

PRO_0000151448

Regions

Domain

109 – 316

208

ATP-grasp

Nucleotide binding

135 – 196

62

ATP By similarity

Sites

Metal binding

286

1

Magnesium or manganese By similarity

Metal binding

288

1

Magnesium or manganese By similarity

Experimental info

Sequence conflict

15 – 16

2

LA → WR in AAA24455. Ref.1

Sequence conflict

97

1

G → V in AAA24455. Ref.1

Secondary structure

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429

Helix Strand Turn

Details...

Beta strand

1 – 7

7

Helix

10 – 19

10

Beta strand

25 – 32

8

Helix

35 – 39

5

Beta strand

43 – 45

3

Helix

53 – 62

10

Beta strand

66 – 70

5

Helix

73 – 77

5

Helix

80 – 86

7

Beta strand

91 – 93

3

Turn

96 – 99

4

Helix

100 – 103

4

Helix

105 – 114

10

Beta strand

122 – 129

8

Helix

130 – 138

9

Beta strand

140 – 145

6

Beta strand

155 – 160

6

Helix

161 – 168

8

Turn

169 – 172

4

Beta strand

184 – 188

5

Beta strand

192 – 204

13

Beta strand

206 – 219

14

Turn

220 – 222

3

Beta strand

223 – 235

13

Helix

241 – 250

10

Helix

252 – 261

10

Beta strand

267 – 277

11

Beta strand

282 – 290

9

Turn

293 – 295

3

Helix

296 – 302

7

Helix

307 – 315

9

Helix

319 – 321

3

Beta strand

328 – 338

11

Turn

339 – 342

4

Beta strand

362 – 371

10

Beta strand

377 – 379

3

Beta strand

381 – 393

13

Helix

394 – 404

11

Turn

405 – 407

3

Helix

421 – 425

5

Sequences

	Sequence		Length	Mass (Da)
	P15640 [UniParc]. Last modified October 1, 1993. Version 2. Checksum: 5E9EFAD478BC1FF4	FASTA	429	45,940
	10 20 30 40 50 60 MKVLVIGNGG REHALAWKAA QSPLVETVFV APGNAGTALE PALQNVAIGV TDIPALLDFA 70 80 90 100 110 120 QNEKIDLTIV GPEAPLVKGV VDTFRAAGLK IFGPTAGAAQ LEGSKAFTKD FLARHKIPTA 130 140 150 160 170 180 EYQNFTEVEP ALAYLREKGA PIVIKADGLA AGKGVIVAMT LEEAEAAVHD MLAGNAFGDA 190 200 210 220 230 240 GHRIVIEEFL DGEEASFIVM VDGEHVLPMA TSQDHKRVGD KDTGPNTGGM GAYSPAPVVT 250 260 270 280 290 300 DDVHQRTMER IIWPTVKGMA AEGNTYTGFL YAGLMIDKQG NPKVIEFNCR FGDPETQPIM 310 320 330 340 350 360 LRMKSDLVEL CLAACESKLD EKTSEWDERA SLGVVMAAGG YPGDYRTGDV IHGLPLEEVA 370 380 390 400 410 420 GGKVFHAGTK LADDEQVVTN GGRVLCVTAL GHTVAEAQKR AYALMTDIHW DDCFCRKDIG WRAIEREQN

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Nucleotide sequence analysis of genes purH and purD involved in the de novo purine nucleotide biosynthesis of Escherichia coli." Aiba A., Mizobuchi K. J. Biol. Chem. 264:21239-21246(1989) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Glycinamide ribonucleotide synthetase from Escherichia coli: cloning, overproduction, sequencing, isolation, and characterization." Shen Y., Rudolph J., Stern M., Flannigan K.A., Smith J.M. Biochemistry 29:218-227(1990) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[3]	"Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes." Blattner F.R., Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L. Nucleic Acids Res. 21:5408-5417(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[5]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[6]	"X-ray crystal structure of glycinamide ribonucleotide synthetase from Escherichia coli." Wang W., Kappock T.J., Stubbe J., Ealick S.E. Biochemistry 37:15647-15662(1998) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

J05126 Genomic DNA. Translation: AAA24455.1.
X51950 Genomic DNA. Translation: CAA36213.1.
U00006 Genomic DNA. Translation: AAC43103.1.
U00096 Genomic DNA. Translation: AAC76979.1.
AP009048 Genomic DNA. Translation: BAE77314.1.

PIR

AJECQG. A33771.

RefSeq

NP_418433.1. NC_000913.2.
YP_491455.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1GSO	X-ray	1.60	A	1-429	[»]

ProteinModelPortal

P15640.

SMR

P15640. Positions 1-426.

ModBase

Search...

Protein-protein interaction databases

IntAct

P15640. 4 interactions.

STRING

511145.b4005.

2D gel databases

SWISS-2DPAGE

P15640.

Proteomic databases

PaxDb

P15640.

PRIDE

P15640.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC76979; AAC76979; b4005.
BAE77314; BAE77314; BAE77314.

GeneID

12933468.
948504.

KEGG

ecj:Y75_p3191.
eco:b4005.

PATRIC

32123535. VBIEscCol129921_4120.

Organism-specific databases

EchoBASE

EB0785.

EcoGene

EG10792. purD.

Phylogenomic databases

eggNOG

COG0151.

HOGENOM

HOG000033463.

KO

K01945.

OMA

MGAYTPL.

ProtClustDB

PRK00885.

Enzyme and pathway databases

BioCyc

EcoCyc:GLYCRIBONUCSYN-MONOMER.
ECOL316407:JW3969-MONOMER.
MetaCyc:GLYCRIBONUCSYN-MONOMER.

UniPathway

UPA00074; UER00125.

Gene expression databases

Genevestigator

P15640.

Family and domain databases

Gene3D

3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
3.40.50.20. 1 hit.
3.90.600.10. 1 hit.

HAMAP

MF_00138. GARS.

InterPro

IPR011761. 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]

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...

Other

EvolutionaryTrace

P15640.

Entry information

Entry name

PUR2_ECOLI

Accession

Primary (citable) accession number: P15640
Secondary accession number(s): Q2M8U2

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1990
Last sequence update:	October 1, 1993
Last modified:	May 1, 2013
This is version 124 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program