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Database: UniProt
Entry: P15640
LinkDB: P15640
Original site: P15640 
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   26-NOV-2014, entry version 134.
DE   RecName: Full=Phosphoribosylamine--glycine ligase;
DE            EC=6.3.4.13;
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; Enterobacteriales;
OC   Enterobacteriaceae; Escherichia.
OX   NCBI_TaxID=83333;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   PubMed=2687276;
RA   Aiba A., Mizobuchi K.;
RT   "Nucleotide sequence analysis of genes purH and purD involved in the
RT   de novo purine nucleotide biosynthesis of Escherichia coli.";
RL   J. Biol. Chem. 264:21239-21246(1989).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
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.,
RA   Daniels D.L.;
RT   "Analysis of the Escherichia coli genome. IV. DNA sequence of the
RT   region 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.,
RA   Mau B., 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
RT   MG1655 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   -!- CATALYTIC ACTIVITY: ATP + 5-phospho-D-ribosylamine + glycine = ADP
CC       + phosphate + N(1)-(5-phospho-D-ribosyl)glycinamide.
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;
CC       N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-alpha-D-
CC       ribose 1-diphosphate: step 2/2.
CC   -!- SUBUNIT: Monomer.
CC   -!- SIMILARITY: Belongs to the GARS family. {ECO:0000305}.
CC   -!- SIMILARITY: Contains 1 ATP-grasp domain. {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; YP_491455.1; NC_007779.1.
DR   PDB; 1GSO; X-ray; 1.60 A; A=1-429.
DR   PDBsum; 1GSO; -.
DR   ProteinModelPortal; P15640; -.
DR   SMR; P15640; 1-426.
DR   IntAct; P15640; 4.
DR   STRING; 511145.b4005; -.
DR   SWISS-2DPAGE; P15640; -.
DR   PaxDb; P15640; -.
DR   PRIDE; P15640; -.
DR   EnsemblBacteria; AAC76979; AAC76979; b4005.
DR   EnsemblBacteria; BAE77314; BAE77314; BAE77314.
DR   GeneID; 12933468; -.
DR   GeneID; 948504; -.
DR   KEGG; ecj:Y75_p3191; -.
DR   KEGG; eco:b4005; -.
DR   PATRIC; 32123535; VBIEscCol129921_4120.
DR   EchoBASE; EB0785; -.
DR   EcoGene; EG10792; purD.
DR   eggNOG; COG0151; -.
DR   HOGENOM; HOG000033463; -.
DR   InParanoid; P15640; -.
DR   KO; K01945; -.
DR   OMA; YKGFLYA; -.
DR   OrthoDB; EOG69SKD1; -.
DR   PhylomeDB; P15640; -.
DR   BioCyc; EcoCyc:GLYCRIBONUCSYN-MONOMER; -.
DR   BioCyc; ECOL316407:JW3969-MONOMER; -.
DR   BioCyc; MetaCyc:GLYCRIBONUCSYN-MONOMER; -.
DR   UniPathway; UPA00074; UER00125.
DR   EvolutionaryTrace; P15640; -.
DR   PRO; PR:P15640; -.
DR   Genevestigator; P15640; -.
DR   GO; GO:0005524; F:ATP binding; IDA:EcoliWiki.
DR   GO; GO:0042623; F:ATPase activity, coupled; IDA:EcoliWiki.
DR   GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-HAMAP.
DR   GO; GO:0030145; F:manganese ion binding; IEA:UniProtKB-HAMAP.
DR   GO; GO:0004637; F:phosphoribosylamine-glycine ligase activity; IDA:EcoCyc.
DR   GO; GO:0006189; P:'de novo' IMP biosynthetic process; IEA:UniProtKB-UniPathway.
DR   GO; GO:0006200; P:ATP catabolic process; IDA:GOC.
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; 3.30.470.20; -; 1.
DR   Gene3D; 3.40.50.20; -; 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; IPR013816; ATP_grasp_subdomain_2.
DR   InterPro; IPR016185; PreATP-grasp_dom.
DR   InterPro; IPR020561; PRibGlycinamid_synth_ATP-grasp.
DR   InterPro; IPR000115; PRibGlycinamide_synth.
DR   InterPro; IPR020560; PRibGlycinamide_synth_C-dom.
DR   InterPro; IPR020559; PRibGlycinamide_synth_CS.
DR   InterPro; IPR020562; PRibGlycinamide_synth_N.
DR   InterPro; IPR011054; Rudment_hybrid_motif.
DR   Pfam; PF01071; GARS_A; 1.
DR   Pfam; PF02843; GARS_C; 1.
DR   Pfam; PF02844; GARS_N; 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; Complete proteome; Ligase; Magnesium;
KW   Manganese; Metal-binding; Nucleotide-binding; Purine biosynthesis;
KW   Reference proteome.
FT   CHAIN         1    429       Phosphoribosylamine--glycine ligase.
FT                                /FTId=PRO_0000151448.
FT   DOMAIN      109    316       ATP-grasp.
FT   NP_BIND     135    196       ATP. {ECO:0000250}.
FT   METAL       286    286       Magnesium or manganese. {ECO:0000250}.
FT   METAL       288    288       Magnesium or manganese. {ECO:0000250}.
FT   CONFLICT     15     16       LA -> WR (in Ref. 1; AAA24455).
FT                                {ECO:0000305}.
FT   CONFLICT     97     97       G -> V (in Ref. 1; AAA24455).
FT                                {ECO:0000305}.
FT   STRAND        1      7       {ECO:0000244|PDB:1GSO}.
FT   HELIX        10     19       {ECO:0000244|PDB:1GSO}.
FT   STRAND       25     32       {ECO:0000244|PDB:1GSO}.
FT   HELIX        35     39       {ECO:0000244|PDB:1GSO}.
FT   STRAND       43     45       {ECO:0000244|PDB:1GSO}.
FT   HELIX        53     62       {ECO:0000244|PDB:1GSO}.
FT   STRAND       66     70       {ECO:0000244|PDB:1GSO}.
FT   HELIX        73     77       {ECO:0000244|PDB:1GSO}.
FT   HELIX        80     86       {ECO:0000244|PDB:1GSO}.
FT   STRAND       91     93       {ECO:0000244|PDB:1GSO}.
FT   TURN         96     99       {ECO:0000244|PDB:1GSO}.
FT   HELIX       100    103       {ECO:0000244|PDB:1GSO}.
FT   HELIX       105    114       {ECO:0000244|PDB:1GSO}.
FT   STRAND      122    129       {ECO:0000244|PDB:1GSO}.
FT   HELIX       130    138       {ECO:0000244|PDB:1GSO}.
FT   STRAND      140    145       {ECO:0000244|PDB:1GSO}.
FT   STRAND      155    160       {ECO:0000244|PDB:1GSO}.
FT   HELIX       161    168       {ECO:0000244|PDB:1GSO}.
FT   TURN        169    172       {ECO:0000244|PDB:1GSO}.
FT   STRAND      184    188       {ECO:0000244|PDB:1GSO}.
FT   STRAND      192    204       {ECO:0000244|PDB:1GSO}.
FT   STRAND      206    219       {ECO:0000244|PDB:1GSO}.
FT   TURN        220    222       {ECO:0000244|PDB:1GSO}.
FT   STRAND      223    235       {ECO:0000244|PDB:1GSO}.
FT   HELIX       241    250       {ECO:0000244|PDB:1GSO}.
FT   HELIX       252    261       {ECO:0000244|PDB:1GSO}.
FT   STRAND      267    277       {ECO:0000244|PDB:1GSO}.
FT   STRAND      282    290       {ECO:0000244|PDB:1GSO}.
FT   TURN        293    295       {ECO:0000244|PDB:1GSO}.
FT   HELIX       296    302       {ECO:0000244|PDB:1GSO}.
FT   HELIX       307    315       {ECO:0000244|PDB:1GSO}.
FT   HELIX       319    321       {ECO:0000244|PDB:1GSO}.
FT   STRAND      328    338       {ECO:0000244|PDB:1GSO}.
FT   TURN        339    342       {ECO:0000244|PDB:1GSO}.
FT   STRAND      362    371       {ECO:0000244|PDB:1GSO}.
FT   STRAND      377    379       {ECO:0000244|PDB:1GSO}.
FT   STRAND      381    393       {ECO:0000244|PDB:1GSO}.
FT   HELIX       394    404       {ECO:0000244|PDB:1GSO}.
FT   TURN        405    407       {ECO:0000244|PDB:1GSO}.
FT   HELIX       421    425       {ECO:0000244|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
//
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