P12039 (PUR2_BACSU) 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:	BSU06530

Organism

Bacillus subtilis (strain 168) [Reference proteome] [HAMAP]

Taxonomic identifier

224308 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Firmicutes › Bacilli › Bacillales › Bacillaceae › Bacillus › Bacillus subtilis group › Bacillus subtilis › Bacillus subtilis subsp. subtilis

Protein attributes

Sequence length	422 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
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
Molecular_function	ATP binding Inferred from electronic annotation. Source: HAMAP magnesium ion binding Inferred from electronic annotation. Source: HAMAP manganese ion binding Inferred from electronic annotation. Source: HAMAP phosphoribosylamine-glycine ligase activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 422

422

Phosphoribosylamine--glycine ligase HAMAP-Rule MF_00138

PRO_0000151436

Regions

Domain

107 – 313

207

ATP-grasp

Nucleotide binding

133 – 194

62

ATP By similarity

Sites

Metal binding

283

1

Magnesium or manganese By similarity

Metal binding

285

1

Magnesium or manganese By similarity

Secondary structure

1

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422

Helix Strand Turn

Details...

Beta strand

2 – 7

6

Helix

10 – 19

10

Beta strand

26 – 32

7

Helix

35 – 37

3

Turn

38 – 40

3

Helix

51 – 60

10

Beta strand

63 – 68

6

Helix

71 – 75

5

Helix

78 – 84

7

Beta strand

89 – 91

3

Turn

94 – 97

4

Helix

98 – 101

4

Helix

103 – 112

10

Beta strand

120 – 124

5

Helix

126 – 136

11

Beta strand

138 – 146

9

Helix

148 – 150

3

Beta strand

153 – 158

6

Helix

159 – 170

12

Helix

176 – 179

4

Beta strand

180 – 186

7

Beta strand

190 – 200

11

Beta strand

203 – 206

4

Beta strand

210 – 217

8

Helix

218 – 220

3

Beta strand

221 – 233

13

Helix

239 – 248

10

Helix

250 – 259

10

Beta strand

265 – 275

11

Beta strand

278 – 287

10

Turn

290 – 292

3

Helix

293 – 296

4

Helix

297 – 299

3

Helix

304 – 312

9

Beta strand

325 – 333

9

Turn

334 – 337

4

Beta strand

345 – 347

3

Beta strand

353 – 365

13

Beta strand

367 – 372

6

Beta strand

374 – 386

13

Helix

387 – 401

15

Helix

414 – 420

7

Sequences

	Sequence		Length	Mass (Da)
	P12039 [UniParc]. Last modified October 1, 1989. Version 1. Checksum: 4EF390A85CC90FB2	FASTA	422	45,280
	10 20 30 40 50 60 MNVLIIGKGG REHTLAWKAA QSSLVENVFA APGNDGMAAS AQLVNIEESD HAGLVSFAKQ 70 80 90 100 110 120 NQVGLTIVGP EVPLIEGLVD EFEKAGLHVF GPSKAAAIIE GSKQFAKDLM KKYDIPTAEY 130 140 150 160 170 180 ETFTSFDEAK AYVQEKGAPI VIKADGLAAG KGVTVAMTEE EAIACLHDFL EDEKFGDASA 190 200 210 220 230 240 SVVIEEYLSG EEFSLMAFVK GEKVYPMVIA QDHKRAFDGD KGPNTGGMGA YSPVPQISEE 250 260 270 280 290 300 TVRHAVETIV KPAAKAMVQE GRSFTGVLYA GLMLTENGSK VIEFNARFGD PETQVVLPRM 310 320 330 340 350 360 ESDLVQVLLD LLDDKEVDLR WKDTAAVSVV LASEGYPESY AKGTPIGSLA AETEQVVVFH 370 380 390 400 410 420 AGTKAEGGEF VTNGGRVANV TAFDETFEAA RDRVYKAVDE IFKPGLFFRK DIGARALKAA QK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning and characterization of a 12-gene cluster from Bacillus subtilis encoding nine enzymes for de novo purine nucleotide synthesis." Ebbole D.J., Zalkin H. J. Biol. Chem. 262:8274-8287(1987) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The 52 degrees-55 degrees segment of the Bacillus subtilis chromosome: a region devoted to purine uptake and metabolism, and containing the genes cotA, gabP and guaA and the pur gene cluster within a 34960 bp nucleotide sequence." Borriss R., Porwollik S., Schroeter R. Microbiology 142:3027-3031(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: 168.
[3]	"The complete genome sequence of the Gram-positive bacterium Bacillus subtilis." Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V. , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A. Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: 168.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

J02732 Genomic DNA. Translation: AAA22684.1.
AF011544 Genomic DNA. Translation: AAB72186.1.
AL009126 Genomic DNA. Translation: CAB12473.1.

PIR

AJBSAG. B29183.

RefSeq

NP_388535.1. NC_000964.3.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2XCL	X-ray	2.10	A	1-422	[»]
2XD4	X-ray	2.65	A	1-422	[»]

ProteinModelPortal

P12039.

SMR

P12039. Positions 1-421.

ModBase

Search...

Protein-protein interaction databases

STRING

224308.BSU06530.

Proteomic databases

PaxDb

P12039.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

CAB12473; CAB12473; BSU06530.

GeneID

938741.

KEGG

bsu:BSU06530.

PATRIC

18972948. VBIBacSub10457_0688.

Organism-specific databases

GenoList

BSU06530. [Micado]

Phylogenomic databases

eggNOG

COG0151.

HOGENOM

HOG000033463.

KO

K01945.

OMA

MGAYTPL.

ProtClustDB

PRK00885.

Enzyme and pathway databases

BioCyc

BSUB:BSU06530-MONOMER.

UniPathway

UPA00074; UER00125.

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...

Entry information

Entry name

PUR2_BACSU

Accession

Primary (citable) accession number: P12039

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1989
Last sequence update:	October 1, 1989
Last modified:	May 1, 2013
This is version 107 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program