PUR2_YERPE
ID PUR2_YERPE Reviewed; 428 AA.
AC Q8ZAR2; Q0WAS9;
DT 27-MAR-2002, integrated into UniProtKB/Swiss-Prot.
DT 27-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 143.
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};
GN OrderedLocusNames=YPO3729, y0501, YP_3092;
OS Yersinia pestis.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Yersiniaceae; Yersinia.
OX NCBI_TaxID=632;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CO-92 / Biovar Orientalis;
RX PubMed=11586360; DOI=10.1038/35097083;
RA Parkhill J., Wren B.W., Thomson N.R., Titball R.W., Holden M.T.G.,
RA Prentice M.B., Sebaihia M., James K.D., Churcher C.M., Mungall K.L.,
RA Baker S., Basham D., Bentley S.D., Brooks K., Cerdeno-Tarraga A.-M.,
RA Chillingworth T., Cronin A., Davies R.M., Davis P., Dougan G., Feltwell T.,
RA Hamlin N., Holroyd S., Jagels K., Karlyshev A.V., Leather S., Moule S.,
RA Oyston P.C.F., Quail M.A., Rutherford K.M., Simmonds M., Skelton J.,
RA Stevens K., Whitehead S., Barrell B.G.;
RT "Genome sequence of Yersinia pestis, the causative agent of plague.";
RL Nature 413:523-527(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=KIM10+ / Biovar Mediaevalis;
RX PubMed=12142430; DOI=10.1128/jb.184.16.4601-4611.2002;
RA Deng W., Burland V., Plunkett G. III, Boutin A., Mayhew G.F., Liss P.,
RA Perna N.T., Rose D.J., Mau B., Zhou S., Schwartz D.C., Fetherston J.D.,
RA Lindler L.E., Brubaker R.R., Plano G.V., Straley S.C., McDonough K.A.,
RA Nilles M.L., Matson J.S., Blattner F.R., Perry R.D.;
RT "Genome sequence of Yersinia pestis KIM.";
RL J. Bacteriol. 184:4601-4611(2002).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=91001 / Biovar Mediaevalis;
RX PubMed=15368893; DOI=10.1093/dnares/11.3.179;
RA Song Y., Tong Z., Wang J., Wang L., Guo Z., Han Y., Zhang J., Pei D.,
RA Zhou D., Qin H., Pang X., Han Y., Zhai J., Li M., Cui B., Qi Z., Jin L.,
RA Dai R., Chen F., Li S., Ye C., Du Z., Lin W., Wang J., Yu J., Yang H.,
RA Wang J., Huang P., Yang R.;
RT "Complete genome sequence of Yersinia pestis strain 91001, an isolate
RT avirulent to humans.";
RL DNA Res. 11:179-197(2004).
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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAM84090.1; Type=Erroneous initiation; Evidence={ECO:0000305};
CC Sequence=AAS63262.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; AL590842; CAL22316.1; -; Genomic_DNA.
DR EMBL; AE009952; AAM84090.1; ALT_INIT; Genomic_DNA.
DR EMBL; AE017042; AAS63262.1; ALT_INIT; Genomic_DNA.
DR PIR; AI0453; AI0453.
DR RefSeq; WP_002210691.1; NZ_WUCM01000097.1.
DR RefSeq; YP_002348609.1; NC_003143.1.
DR PDB; 3MJF; X-ray; 1.47 A; A=1-428.
DR PDBsum; 3MJF; -.
DR AlphaFoldDB; Q8ZAR2; -.
DR SMR; Q8ZAR2; -.
DR IntAct; Q8ZAR2; 6.
DR STRING; 214092.YPO3729; -.
DR PaxDb; Q8ZAR2; -.
DR DNASU; 1145448; -.
DR EnsemblBacteria; AAM84090; AAM84090; y0501.
DR EnsemblBacteria; AAS63262; AAS63262; YP_3092.
DR GeneID; 57974988; -.
DR KEGG; ype:YPO3729; -.
DR KEGG; ypk:y0501; -.
DR KEGG; ypm:YP_3092; -.
DR PATRIC; fig|214092.21.peg.4247; -.
DR eggNOG; COG0151; Bacteria.
DR HOGENOM; CLU_027420_3_1_6; -.
DR OMA; KATVCKY; -.
DR UniPathway; UPA00074; UER00125.
DR EvolutionaryTrace; Q8ZAR2; -.
DR Proteomes; UP000000815; Chromosome.
DR Proteomes; UP000001019; Chromosome.
DR Proteomes; UP000002490; 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..428
FT /note="Phosphoribosylamine--glycine ligase"
FT /id="PRO_0000151506"
FT DOMAIN 109..316
FT /note="ATP-grasp"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00138"
FT BINDING 135..196
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00138"
FT BINDING 286
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00138"
FT BINDING 288
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00138"
FT STRAND 1..7
FT /evidence="ECO:0007829|PDB:3MJF"
FT HELIX 10..19
FT /evidence="ECO:0007829|PDB:3MJF"
FT STRAND 25..32
FT /evidence="ECO:0007829|PDB:3MJF"
FT HELIX 35..39
FT /evidence="ECO:0007829|PDB:3MJF"
FT HELIX 53..62
FT /evidence="ECO:0007829|PDB:3MJF"
FT STRAND 65..70
FT /evidence="ECO:0007829|PDB:3MJF"
FT HELIX 73..77
FT /evidence="ECO:0007829|PDB:3MJF"
FT HELIX 80..86
FT /evidence="ECO:0007829|PDB:3MJF"
FT STRAND 91..93
FT /evidence="ECO:0007829|PDB:3MJF"
FT HELIX 96..103
FT /evidence="ECO:0007829|PDB:3MJF"
FT HELIX 105..114
FT /evidence="ECO:0007829|PDB:3MJF"
FT STRAND 122..126
FT /evidence="ECO:0007829|PDB:3MJF"
FT HELIX 128..138
FT /evidence="ECO:0007829|PDB:3MJF"
FT STRAND 140..149
FT /evidence="ECO:0007829|PDB:3MJF"
FT STRAND 154..158
FT /evidence="ECO:0007829|PDB:3MJF"
FT HELIX 161..172
FT /evidence="ECO:0007829|PDB:3MJF"
FT HELIX 175..178
FT /evidence="ECO:0007829|PDB:3MJF"
FT STRAND 184..188
FT /evidence="ECO:0007829|PDB:3MJF"
FT STRAND 192..204
FT /evidence="ECO:0007829|PDB:3MJF"
FT STRAND 206..208
FT /evidence="ECO:0007829|PDB:3MJF"
FT STRAND 212..214
FT /evidence="ECO:0007829|PDB:3MJF"
FT STRAND 217..219
FT /evidence="ECO:0007829|PDB:3MJF"
FT TURN 220..222
FT /evidence="ECO:0007829|PDB:3MJF"
FT STRAND 223..226
FT /evidence="ECO:0007829|PDB:3MJF"
FT STRAND 230..235
FT /evidence="ECO:0007829|PDB:3MJF"
FT HELIX 241..250
FT /evidence="ECO:0007829|PDB:3MJF"
FT HELIX 252..261
FT /evidence="ECO:0007829|PDB:3MJF"
FT STRAND 267..276
FT /evidence="ECO:0007829|PDB:3MJF"
FT STRAND 282..287
FT /evidence="ECO:0007829|PDB:3MJF"
FT HELIX 289..291
FT /evidence="ECO:0007829|PDB:3MJF"
FT TURN 293..295
FT /evidence="ECO:0007829|PDB:3MJF"
FT HELIX 296..302
FT /evidence="ECO:0007829|PDB:3MJF"
FT HELIX 307..315
FT /evidence="ECO:0007829|PDB:3MJF"
FT HELIX 319..321
FT /evidence="ECO:0007829|PDB:3MJF"
FT STRAND 331..338
FT /evidence="ECO:0007829|PDB:3MJF"
FT TURN 339..342
FT /evidence="ECO:0007829|PDB:3MJF"
FT STRAND 362..371
FT /evidence="ECO:0007829|PDB:3MJF"
FT STRAND 377..379
FT /evidence="ECO:0007829|PDB:3MJF"
FT STRAND 381..390
FT /evidence="ECO:0007829|PDB:3MJF"
FT HELIX 394..405
FT /evidence="ECO:0007829|PDB:3MJF"
FT HELIX 421..424
FT /evidence="ECO:0007829|PDB:3MJF"
FT TURN 425..427
FT /evidence="ECO:0007829|PDB:3MJF"
SQ SEQUENCE 428 AA; 45317 MW; 0D12863DD2424EFF CRC64;
MNILIIGNGG REHALGWKAA QSPLADKIYV APGNAGTALE PTLENVDIAA TDIAGLLAFA
QSHDIGLTIV GPEAPLVIGV VDAFRAAGLA IFGPTQAAAQ LEGSKAFTKD FLARHNIPSA
EYQNFTDVEA ALAYVRQKGA PIVIKADGLA AGKGVIVAMT QEEAETAVND MLAGNAFGDA
GHRIVVEEFL DGEEASFIVM VDGENVLPMA TSQDHKRVGD GDTGPNTGGM GAYSPAPVVT
DDVHQRVMDQ VIWPTVRGMA AEGNIYTGFL YAGLMISADG QPKVIEFNCR FGDPETQPIM
LRMRSDLVEL CLAGTQGKLN EKTSDWDERP SLGVVLAAGG YPADYRQGDV IHGLPQQEVK
DGKVFHAGTK LNGNHEVVTN GGRVLCVTAL GETVAQAQQY AYQLAEGIQW EGVFCRKDIG
YRAIARGK
