PUR2_ECOLI
ID PUR2_ECOLI Reviewed; 429 AA.
AC P15640; Q2M8U2;
DT 01-APR-1990, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1993, sequence version 2.
DT 03-AUG-2022, entry version 176.
DE RecName: Full=Phosphoribosylamine--glycine ligase;
DE EC=6.3.4.13 {ECO:0000269|PubMed:2182115};
DE AltName: Full=GARS;
DE AltName: Full=Glycinamide ribonucleotide synthetase;
DE AltName: Full=Phosphoribosylglycinamide synthetase;
GN Name=purD; OrderedLocusNames=b4005, JW3969;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2687276; DOI=10.1016/s0021-9258(19)30072-9;
RA Aiba A., Mizobuchi K.;
RT "Nucleotide sequence analysis of genes purH and purD involved in the de
RT novo purine nucleotide biosynthesis of Escherichia coli.";
RL J. Biol. Chem. 264:21239-21246(1989).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-15, FUNCTION,
RP CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, COFACTOR, AND
RP PATHWAY.
RC STRAIN=K12;
RX PubMed=2182115; DOI=10.1021/bi00453a030;
RA Shen Y., Rudolph J., Stern M., Flannigan K.A., Smith J.M.;
RT "Glycinamide ribonucleotide synthetase from Escherichia coli: cloning,
RT overproduction, sequencing, isolation, and characterization.";
RL Biochemistry 29:218-227(1990).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=8265357; DOI=10.1093/nar/21.23.5408;
RA Blattner F.R., Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L.;
RT "Analysis of the Escherichia coli genome. IV. DNA sequence of the region
RT from 89.2 to 92.8 minutes.";
RL Nucleic Acids Res. 21:5408-5417(1993).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
RX PubMed=9843369; DOI=10.1021/bi981405n;
RA Wang W., Kappock T.J., Stubbe J., Ealick S.E.;
RT "X-ray crystal structure of glycinamide ribonucleotide synthetase from
RT Escherichia coli.";
RL Biochemistry 37:15647-15662(1998).
CC -!- FUNCTION: Catalyzes the reversible conversion of phosphoribosylamine to
CC glycinamide ribonucleotide, an enzymatic step in purine biosynthesis
CC pathway. {ECO:0000269|PubMed:2182115}.
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:0000269|PubMed:2182115};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:17454;
CC Evidence={ECO:0000269|PubMed:2182115};
CC PhysiologicalDirection=right-to-left; Xref=Rhea:RHEA:17455;
CC Evidence={ECO:0000269|PubMed:2182115};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:2182115};
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 -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=70 uM for 5-phospho-beta-D-ribosylamine
CC {ECO:0000269|PubMed:2182115};
CC KM=270 uM for glycine {ECO:0000269|PubMed:2182115};
CC KM=170 uM for ATP {ECO:0000269|PubMed:2182115};
CC KM=30 uM for N(1)-(5-phospho-beta-D-ribosyl)glycinamide
CC {ECO:0000269|PubMed:2182115};
CC KM=6.4 uM for ADP {ECO:0000269|PubMed:2182115};
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:0000305|PubMed:2182115}.
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:2182115}.
CC -!- SIMILARITY: Belongs to the GARS family. {ECO:0000305}.
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DR EMBL; J05126; AAA24455.1; -; Genomic_DNA.
DR EMBL; X51950; CAA36213.1; -; Genomic_DNA.
DR EMBL; U00006; AAC43103.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76979.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77314.1; -; Genomic_DNA.
DR PIR; A33771; AJECQG.
DR RefSeq; NP_418433.1; NC_000913.3.
DR RefSeq; WP_000866800.1; NZ_SSZK01000047.1.
DR PDB; 1GSO; X-ray; 1.60 A; A=1-429.
DR PDBsum; 1GSO; -.
DR AlphaFoldDB; P15640; -.
DR SMR; P15640; -.
DR BioGRID; 4262462; 50.
DR IntAct; P15640; 4.
DR STRING; 511145.b4005; -.
DR SWISS-2DPAGE; P15640; -.
DR jPOST; P15640; -.
DR PaxDb; P15640; -.
DR PRIDE; P15640; -.
DR EnsemblBacteria; AAC76979; AAC76979; b4005.
DR EnsemblBacteria; BAE77314; BAE77314; BAE77314.
DR GeneID; 948504; -.
DR KEGG; ecj:JW3969; -.
DR KEGG; eco:b4005; -.
DR PATRIC; fig|1411691.4.peg.2705; -.
DR EchoBASE; EB0785; -.
DR eggNOG; COG0151; Bacteria.
DR HOGENOM; CLU_027420_3_1_6; -.
DR InParanoid; P15640; -.
DR OMA; KATVCKY; -.
DR PhylomeDB; P15640; -.
DR BioCyc; EcoCyc:GLYCRIBONUCSYN-MON; -.
DR BioCyc; MetaCyc:GLYCRIBONUCSYN-MON; -.
DR BRENDA; 6.3.4.13; 2026.
DR UniPathway; UPA00074; UER00125.
DR EvolutionaryTrace; P15640; -.
DR PRO; PR:P15640; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005524; F:ATP binding; IDA:EcoliWiki.
DR GO; GO:0016887; F:ATP hydrolysis activity; IDA:EcoliWiki.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004637; F:phosphoribosylamine-glycine ligase activity; IDA:EcoCyc.
DR GO; GO:0006189; P:'de novo' IMP biosynthetic process; IEA:UniProtKB-UniRule.
DR GO; GO:0006974; P:cellular response to DNA damage stimulus; IEP:EcoliWiki.
DR GO; GO:0009113; P:purine nucleobase biosynthetic process; IEA:InterPro.
DR GO; GO:0006164; P:purine nucleotide biosynthetic process; NAS:EcoliWiki.
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; Direct protein sequencing; Ligase; Magnesium;
KW Manganese; Metal-binding; Nucleotide-binding; Purine biosynthesis;
KW Reference proteome.
FT CHAIN 1..429
FT /note="Phosphoribosylamine--glycine ligase"
FT /id="PRO_0000151448"
FT DOMAIN 109..316
FT /note="ATP-grasp"
FT REGION 212..236
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 135..196
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 286
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 288
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT CONFLICT 15..16
FT /note="LA -> WR (in Ref. 1; AAA24455)"
FT /evidence="ECO:0000305"
FT CONFLICT 97
FT /note="G -> V (in Ref. 1; AAA24455)"
FT /evidence="ECO:0000305"
FT STRAND 1..7
FT /evidence="ECO:0007829|PDB:1GSO"
FT HELIX 10..19
FT /evidence="ECO:0007829|PDB:1GSO"
FT STRAND 25..32
FT /evidence="ECO:0007829|PDB:1GSO"
FT HELIX 35..39
FT /evidence="ECO:0007829|PDB:1GSO"
FT STRAND 43..45
FT /evidence="ECO:0007829|PDB:1GSO"
FT HELIX 53..62
FT /evidence="ECO:0007829|PDB:1GSO"
FT STRAND 66..70
FT /evidence="ECO:0007829|PDB:1GSO"
FT HELIX 73..77
FT /evidence="ECO:0007829|PDB:1GSO"
FT HELIX 80..86
FT /evidence="ECO:0007829|PDB:1GSO"
FT STRAND 91..93
FT /evidence="ECO:0007829|PDB:1GSO"
FT TURN 96..99
FT /evidence="ECO:0007829|PDB:1GSO"
FT HELIX 100..103
FT /evidence="ECO:0007829|PDB:1GSO"
FT HELIX 105..114
FT /evidence="ECO:0007829|PDB:1GSO"
FT STRAND 122..129
FT /evidence="ECO:0007829|PDB:1GSO"
FT HELIX 130..138
FT /evidence="ECO:0007829|PDB:1GSO"
FT STRAND 140..145
FT /evidence="ECO:0007829|PDB:1GSO"
FT STRAND 155..160
FT /evidence="ECO:0007829|PDB:1GSO"
FT HELIX 161..168
FT /evidence="ECO:0007829|PDB:1GSO"
FT TURN 169..172
FT /evidence="ECO:0007829|PDB:1GSO"
FT STRAND 184..188
FT /evidence="ECO:0007829|PDB:1GSO"
FT STRAND 192..204
FT /evidence="ECO:0007829|PDB:1GSO"
FT STRAND 206..219
FT /evidence="ECO:0007829|PDB:1GSO"
FT TURN 220..222
FT /evidence="ECO:0007829|PDB:1GSO"
FT STRAND 223..235
FT /evidence="ECO:0007829|PDB:1GSO"
FT HELIX 241..250
FT /evidence="ECO:0007829|PDB:1GSO"
FT HELIX 252..261
FT /evidence="ECO:0007829|PDB:1GSO"
FT STRAND 267..277
FT /evidence="ECO:0007829|PDB:1GSO"
FT STRAND 282..290
FT /evidence="ECO:0007829|PDB:1GSO"
FT TURN 293..295
FT /evidence="ECO:0007829|PDB:1GSO"
FT HELIX 296..302
FT /evidence="ECO:0007829|PDB:1GSO"
FT HELIX 307..315
FT /evidence="ECO:0007829|PDB:1GSO"
FT HELIX 319..321
FT /evidence="ECO:0007829|PDB:1GSO"
FT STRAND 328..338
FT /evidence="ECO:0007829|PDB:1GSO"
FT TURN 339..342
FT /evidence="ECO:0007829|PDB:1GSO"
FT STRAND 362..371
FT /evidence="ECO:0007829|PDB:1GSO"
FT STRAND 377..379
FT /evidence="ECO:0007829|PDB:1GSO"
FT STRAND 381..393
FT /evidence="ECO:0007829|PDB:1GSO"
FT HELIX 394..404
FT /evidence="ECO:0007829|PDB:1GSO"
FT TURN 405..407
FT /evidence="ECO:0007829|PDB:1GSO"
FT HELIX 421..425
FT /evidence="ECO:0007829|PDB:1GSO"
SQ SEQUENCE 429 AA; 45940 MW; 5E9EFAD478BC1FF4 CRC64;
MKVLVIGNGG REHALAWKAA QSPLVETVFV APGNAGTALE PALQNVAIGV TDIPALLDFA
QNEKIDLTIV GPEAPLVKGV VDTFRAAGLK IFGPTAGAAQ LEGSKAFTKD FLARHKIPTA
EYQNFTEVEP ALAYLREKGA PIVIKADGLA AGKGVIVAMT LEEAEAAVHD MLAGNAFGDA
GHRIVIEEFL DGEEASFIVM VDGEHVLPMA TSQDHKRVGD KDTGPNTGGM GAYSPAPVVT
DDVHQRTMER IIWPTVKGMA AEGNTYTGFL YAGLMIDKQG NPKVIEFNCR FGDPETQPIM
LRMKSDLVEL CLAACESKLD EKTSEWDERA SLGVVMAAGG YPGDYRTGDV IHGLPLEEVA
GGKVFHAGTK LADDEQVVTN GGRVLCVTAL GHTVAEAQKR AYALMTDIHW DDCFCRKDIG
WRAIEREQN
