PUR2_BACSU
ID PUR2_BACSU Reviewed; 422 AA.
AC P12039;
DT 01-OCT-1989, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1989, sequence version 1.
DT 03-AUG-2022, entry version 147.
DE RecName: Full=Phosphoribosylamine--glycine ligase {ECO:0000255|HAMAP-Rule:MF_00138};
DE EC=6.3.4.13 {ECO:0000255|HAMAP-Rule:MF_00138};
DE AltName: Full=GARS {ECO:0000255|HAMAP-Rule:MF_00138};
DE AltName: Full=Glycinamide ribonucleotide synthetase {ECO:0000255|HAMAP-Rule:MF_00138};
DE AltName: Full=Phosphoribosylglycinamide synthetase {ECO:0000255|HAMAP-Rule:MF_00138};
GN Name=purD {ECO:0000255|HAMAP-Rule:MF_00138}; OrderedLocusNames=BSU06530;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=3036807; DOI=10.1016/s0021-9258(18)47560-6;
RA Ebbole D.J., Zalkin H.;
RT "Cloning and characterization of a 12-gene cluster from Bacillus subtilis
RT encoding nine enzymes for de novo purine nucleotide synthesis.";
RL J. Biol. Chem. 262:8274-8287(1987).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RX PubMed=8969499; DOI=10.1099/13500872-142-11-3027;
RA Borriss R., Porwollik S., Schroeter R.;
RT "The 52 degrees-55 degrees segment of the Bacillus subtilis chromosome: a
RT region devoted to purine uptake and metabolism, and containing the genes
RT cotA, gabP and guaA and the pur gene cluster within a 34960 bp nucleotide
RT sequence.";
RL Microbiology 142:3027-3031(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5-phospho-beta-D-ribosylamine + ATP + glycine = ADP + H(+) +
CC N(1)-(5-phospho-beta-D-ribosyl)glycinamide + phosphate;
CC Xref=Rhea:RHEA:17453, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:57305, ChEBI:CHEBI:58681,
CC ChEBI:CHEBI:143788, ChEBI:CHEBI:456216; EC=6.3.4.13;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00138};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC Note=Binds 1 Mg(2+) or Mn(2+) ion per subunit. {ECO:0000250};
CC -!- PATHWAY: Purine metabolism; IMP biosynthesis via de novo pathway; N(1)-
CC (5-phospho-D-ribosyl)glycinamide from 5-phospho-alpha-D-ribose 1-
CC diphosphate: step 2/2. {ECO:0000255|HAMAP-Rule:MF_00138}.
CC -!- SIMILARITY: Belongs to the GARS family. {ECO:0000255|HAMAP-
CC Rule:MF_00138}.
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DR EMBL; J02732; AAA22684.1; -; Genomic_DNA.
DR EMBL; AF011544; AAB72186.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB12473.1; -; Genomic_DNA.
DR PIR; B29183; AJBSAG.
DR RefSeq; NP_388535.1; NC_000964.3.
DR RefSeq; WP_003242993.1; NZ_JNCM01000032.1.
DR PDB; 2XCL; X-ray; 2.10 A; A=1-422.
DR PDB; 2XD4; X-ray; 2.65 A; A=1-422.
DR PDBsum; 2XCL; -.
DR PDBsum; 2XD4; -.
DR AlphaFoldDB; P12039; -.
DR SMR; P12039; -.
DR STRING; 224308.BSU06530; -.
DR PaxDb; P12039; -.
DR PRIDE; P12039; -.
DR EnsemblBacteria; CAB12473; CAB12473; BSU_06530.
DR GeneID; 938741; -.
DR KEGG; bsu:BSU06530; -.
DR PATRIC; fig|224308.179.peg.709; -.
DR eggNOG; COG0151; Bacteria.
DR InParanoid; P12039; -.
DR OMA; KATVCKY; -.
DR PhylomeDB; P12039; -.
DR BioCyc; BSUB:BSU06530-MON; -.
DR UniPathway; UPA00074; UER00125.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004637; F:phosphoribosylamine-glycine ligase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0006189; P:'de novo' IMP biosynthetic process; IEA:UniProtKB-UniRule.
DR GO; GO:0009113; P:purine nucleobase biosynthetic process; IEA:InterPro.
DR Gene3D; 3.30.1490.20; -; 1.
DR Gene3D; 3.90.600.10; -; 1.
DR HAMAP; MF_00138; GARS; 1.
DR InterPro; IPR011761; ATP-grasp.
DR InterPro; IPR013815; ATP_grasp_subdomain_1.
DR InterPro; IPR016185; PreATP-grasp_dom_sf.
DR InterPro; IPR020561; PRibGlycinamid_synth_ATP-grasp.
DR InterPro; IPR000115; PRibGlycinamide_synth.
DR InterPro; IPR020560; PRibGlycinamide_synth_C-dom.
DR InterPro; IPR037123; PRibGlycinamide_synth_C_sf.
DR InterPro; IPR020559; PRibGlycinamide_synth_CS.
DR InterPro; IPR020562; PRibGlycinamide_synth_N.
DR InterPro; IPR011054; Rudment_hybrid_motif.
DR PANTHER; PTHR43472; PTHR43472; 1.
DR Pfam; PF01071; GARS_A; 1.
DR Pfam; PF02843; GARS_C; 1.
DR Pfam; PF02844; GARS_N; 1.
DR SMART; SM01210; GARS_C; 1.
DR SUPFAM; SSF51246; SSF51246; 1.
DR SUPFAM; SSF52440; SSF52440; 1.
DR TIGRFAMs; TIGR00877; purD; 1.
DR PROSITE; PS50975; ATP_GRASP; 1.
DR PROSITE; PS00184; GARS; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Ligase; Magnesium; Manganese; Metal-binding;
KW Nucleotide-binding; Purine biosynthesis; Reference proteome.
FT CHAIN 1..422
FT /note="Phosphoribosylamine--glycine ligase"
FT /id="PRO_0000151436"
FT DOMAIN 107..313
FT /note="ATP-grasp"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00138"
FT BINDING 133..194
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00138"
FT BINDING 283
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00138"
FT BINDING 285
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00138"
FT STRAND 2..7
FT /evidence="ECO:0007829|PDB:2XCL"
FT HELIX 10..19
FT /evidence="ECO:0007829|PDB:2XCL"
FT STRAND 26..32
FT /evidence="ECO:0007829|PDB:2XCL"
FT HELIX 35..37
FT /evidence="ECO:0007829|PDB:2XCL"
FT TURN 38..40
FT /evidence="ECO:0007829|PDB:2XCL"
FT HELIX 51..60
FT /evidence="ECO:0007829|PDB:2XCL"
FT STRAND 63..68
FT /evidence="ECO:0007829|PDB:2XCL"
FT HELIX 71..75
FT /evidence="ECO:0007829|PDB:2XCL"
FT HELIX 78..84
FT /evidence="ECO:0007829|PDB:2XCL"
FT STRAND 89..91
FT /evidence="ECO:0007829|PDB:2XCL"
FT TURN 94..97
FT /evidence="ECO:0007829|PDB:2XCL"
FT HELIX 98..101
FT /evidence="ECO:0007829|PDB:2XCL"
FT HELIX 103..112
FT /evidence="ECO:0007829|PDB:2XCL"
FT STRAND 120..124
FT /evidence="ECO:0007829|PDB:2XCL"
FT HELIX 126..136
FT /evidence="ECO:0007829|PDB:2XCL"
FT STRAND 138..146
FT /evidence="ECO:0007829|PDB:2XCL"
FT HELIX 148..150
FT /evidence="ECO:0007829|PDB:2XCL"
FT STRAND 153..158
FT /evidence="ECO:0007829|PDB:2XCL"
FT HELIX 159..170
FT /evidence="ECO:0007829|PDB:2XCL"
FT HELIX 176..179
FT /evidence="ECO:0007829|PDB:2XCL"
FT STRAND 180..186
FT /evidence="ECO:0007829|PDB:2XCL"
FT STRAND 190..200
FT /evidence="ECO:0007829|PDB:2XCL"
FT STRAND 203..206
FT /evidence="ECO:0007829|PDB:2XCL"
FT STRAND 210..217
FT /evidence="ECO:0007829|PDB:2XCL"
FT HELIX 218..220
FT /evidence="ECO:0007829|PDB:2XCL"
FT STRAND 221..233
FT /evidence="ECO:0007829|PDB:2XCL"
FT HELIX 239..248
FT /evidence="ECO:0007829|PDB:2XCL"
FT HELIX 250..259
FT /evidence="ECO:0007829|PDB:2XCL"
FT STRAND 265..275
FT /evidence="ECO:0007829|PDB:2XCL"
FT STRAND 278..287
FT /evidence="ECO:0007829|PDB:2XCL"
FT TURN 290..292
FT /evidence="ECO:0007829|PDB:2XCL"
FT HELIX 293..296
FT /evidence="ECO:0007829|PDB:2XCL"
FT HELIX 297..299
FT /evidence="ECO:0007829|PDB:2XCL"
FT HELIX 304..312
FT /evidence="ECO:0007829|PDB:2XCL"
FT STRAND 325..333
FT /evidence="ECO:0007829|PDB:2XCL"
FT TURN 334..337
FT /evidence="ECO:0007829|PDB:2XCL"
FT STRAND 345..347
FT /evidence="ECO:0007829|PDB:2XD4"
FT STRAND 353..365
FT /evidence="ECO:0007829|PDB:2XCL"
FT STRAND 367..372
FT /evidence="ECO:0007829|PDB:2XCL"
FT STRAND 374..386
FT /evidence="ECO:0007829|PDB:2XCL"
FT HELIX 387..401
FT /evidence="ECO:0007829|PDB:2XCL"
FT HELIX 414..420
FT /evidence="ECO:0007829|PDB:2XCL"
SQ SEQUENCE 422 AA; 45280 MW; 4EF390A85CC90FB2 CRC64;
MNVLIIGKGG REHTLAWKAA QSSLVENVFA APGNDGMAAS AQLVNIEESD HAGLVSFAKQ
NQVGLTIVGP EVPLIEGLVD EFEKAGLHVF GPSKAAAIIE GSKQFAKDLM KKYDIPTAEY
ETFTSFDEAK AYVQEKGAPI VIKADGLAAG KGVTVAMTEE EAIACLHDFL EDEKFGDASA
SVVIEEYLSG EEFSLMAFVK GEKVYPMVIA QDHKRAFDGD KGPNTGGMGA YSPVPQISEE
TVRHAVETIV KPAAKAMVQE GRSFTGVLYA GLMLTENGSK VIEFNARFGD PETQVVLPRM
ESDLVQVLLD LLDDKEVDLR WKDTAAVSVV LASEGYPESY AKGTPIGSLA AETEQVVVFH
AGTKAEGGEF VTNGGRVANV TAFDETFEAA RDRVYKAVDE IFKPGLFFRK DIGARALKAA
QK
