PUR3_ECOLI
ID PUR3_ECOLI Reviewed; 212 AA.
AC P08179;
DT 01-AUG-1988, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1988, sequence version 1.
DT 03-AUG-2022, entry version 184.
DE RecName: Full=Phosphoribosylglycinamide formyltransferase {ECO:0000255|HAMAP-Rule:MF_01930};
DE EC=2.1.2.2 {ECO:0000255|HAMAP-Rule:MF_01930, ECO:0000269|PubMed:2185839, ECO:0000269|PubMed:350869};
DE AltName: Full=5'-phosphoribosylglycinamide transformylase {ECO:0000255|HAMAP-Rule:MF_01930};
DE AltName: Full=GAR transformylase {ECO:0000255|HAMAP-Rule:MF_01930};
DE Short=GART {ECO:0000255|HAMAP-Rule:MF_01930};
GN Name=purN {ECO:0000255|HAMAP-Rule:MF_01930, ECO:0000303|PubMed:3301838};
GN OrderedLocusNames=b2500, JW2485;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=3301838; DOI=10.1016/s0021-9258(18)60999-8;
RA Smith J.M., Daum H.A. III;
RT "Identification and nucleotide sequence of a gene encoding 5'-
RT phosphoribosylglycinamide transformylase in Escherichia coli K12.";
RL J. Biol. Chem. 262:10565-10569(1987).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9205837; DOI=10.1093/dnares/4.2.91;
RA Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K.,
RA Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T., Oyama S.,
RA Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H.,
RA Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.;
RT "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12
RT genome corresponding to 50.0-68.8 min on the linkage map and analysis of
RT its sequence features.";
RL DNA Res. 4:91-113(1997).
RN [3]
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 [4]
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 [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ECOR 7;
RX PubMed=10954745; DOI=10.1073/pnas.180094797;
RA Pupo G.M., Lan R., Reeves P.R.;
RT "Multiple independent origins of Shigella clones of Escherichia coli and
RT convergent evolution of many of their characteristics.";
RL Proc. Natl. Acad. Sci. U.S.A. 97:10567-10572(2000).
RN [6]
RP PROTEIN SEQUENCE OF 1-6, FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RX PubMed=2185839; DOI=10.1021/bi00458a014;
RA Inglese J., Johnson D.L., Shiau A., Smith J.M., Benkovic S.J.;
RT "Subcloning, characterization, and affinity labeling of Escherichia coli
RT glycinamide ribonucleotide transformylase.";
RL Biochemistry 29:1436-1443(1990).
RN [7]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=350869; DOI=10.1016/s0021-9258(17)34710-5;
RA Dev I.K., Harvey R.J.;
RT "N10-Formyltetrahydrofolate is the formyl donor for glycinamide ribotide
RT transformylase in Escherichia coli.";
RL J. Biol. Chem. 253:4242-4244(1978).
RN [8]
RP MUTAGENESIS OF ASP-144, AND PARTIAL PROTEIN SEQUENCE.
RX PubMed=2204419; DOI=10.1021/bi00480a018;
RA Inglese J., Smith J.M., Benkovic S.J.;
RT "Active-site mapping and site-specific mutagenesis of glycinamide
RT ribonucleotide transformylase from Escherichia coli.";
RL Biochemistry 29:6678-6687(1990).
RN [9]
RP MUTAGENESIS OF ASN-106; HIS-108; HIS-119; SER-135; HIS-137 AND ASP-144, AND
RP PATHWAY.
RX PubMed=8688421; DOI=10.1021/bi9528715;
RA Warren M.S., Marolewski A.E., Benkovic S.J.;
RT "A rapid screen of active site mutants in glycinamide ribonucleotide
RT transformylase.";
RL Biochemistry 35:8855-8862(1996).
RN [10]
RP MUTAGENESIS OF HIS-108; HIS-121 AND ASP-144, AND ACTIVE SITE.
RX PubMed=10433709; DOI=10.1021/bi9904609;
RA Shim J.H., Benkovic S.J.;
RT "Catalytic mechanism of Escherichia coli glycinamide ribonucleotide
RT transformylase probed by site-directed mutagenesis and pH-dependent
RT studies.";
RL Biochemistry 38:10024-10031(1999).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG.
RX PubMed=1522592; DOI=10.1016/0022-2836(92)90698-j;
RA Chen P., Schulze-Gahmen U., Stura E.A., Inglese J., Johnson D.L.,
RA Marolewski A., Benkovic S.J., Wilson I.A.;
RT "Crystal structure of glycinamide ribonucleotide transformylase from
RT Escherichia coli at 3.0-A resolution. A target enzyme for chemotherapy.";
RL J. Mol. Biol. 227:283-292(1992).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS.
RX PubMed=1631098; DOI=10.1073/pnas.89.13.6114;
RA Almassy R.J., Janson C.A., Kan C.-C., Hostomska Z.;
RT "Structures of apo and complexed Escherichia coli glycinamide
RT ribonucleotide transformylase.";
RL Proc. Natl. Acad. Sci. U.S.A. 89:6114-6118(1992).
RN [13]
RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF MUTANT ALA-70 IN COMPLEX WITH
RP SUBSTRATE ANALOGS, AND SUBUNIT.
RX PubMed=9698564; DOI=10.1006/jmbi.1998.1931;
RA Su Y., Yamashita M.M., Greasley S.E., Mullen C.A., Shim J.H.,
RA Jennings P.A., Benkovic S.J., Wilson I.A.;
RT "A pH-dependent stabilization of an active site loop observed from low and
RT high pH crystal structures of mutant monomeric glycinamide ribonucleotide
RT transformylase at 1.8 to 1.9 A.";
RL J. Mol. Biol. 281:485-499(1998).
RN [14]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS.
RX PubMed=10606510; DOI=10.1021/bi991888a;
RA Greasley S.E., Yamashita M.M., Cai H., Benkovic S.J., Boger D.L.,
RA Wilson I.A.;
RT "New insights into inhibitor design from the crystal structure and NMR
RT studies of Escherichia coli GAR transformylase in complex with beta-GAR and
RT 10-formyl-5,8,10-trideazafolic acid.";
RL Biochemistry 38:16783-16793(1999).
CC -!- FUNCTION: Catalyzes the transfer of a formyl group from 10-
CC formyltetrahydrofolate to 5-phospho-ribosyl-glycinamide (GAR),
CC producing 5-phospho-ribosyl-N-formylglycinamide (FGAR) and
CC tetrahydrofolate. {ECO:0000255|HAMAP-Rule:MF_01930,
CC ECO:0000269|PubMed:2185839, ECO:0000269|PubMed:350869}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(6S)-10-formyltetrahydrofolate + N(1)-(5-phospho-beta-D-
CC ribosyl)glycinamide = (6S)-5,6,7,8-tetrahydrofolate + H(+) + N(2)-
CC formyl-N(1)-(5-phospho-beta-D-ribosyl)glycinamide;
CC Xref=Rhea:RHEA:15053, ChEBI:CHEBI:15378, ChEBI:CHEBI:57453,
CC ChEBI:CHEBI:57454, ChEBI:CHEBI:143788, ChEBI:CHEBI:147286;
CC EC=2.1.2.2; Evidence={ECO:0000255|HAMAP-Rule:MF_01930,
CC ECO:0000269|PubMed:2185839, ECO:0000269|PubMed:350869};
CC -!- ACTIVITY REGULATION: Inhibited by N10-(bromoacetyl)-5,8-dideazafolate.
CC {ECO:0000269|PubMed:2185839}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=77.5 uM for (6R)-N10-formyltetrahydrofolate (at pH 8.5)
CC {ECO:0000269|PubMed:2185839};
CC KM=84.8 uM for (6R)-N10-formyltetrahydrofolate (at pH 7.5)
CC {ECO:0000269|PubMed:2185839};
CC Note=kcat is 20.7 sec(-1) for (6R)-N10-formyltetrahydrofolate (at pH
CC 8.5). kcat is 13.5 sec(-1) for (6R)-N10-formyltetrahydrofolate (at pH
CC 7.5). {ECO:0000269|PubMed:2185839};
CC pH dependence:
CC Optimum pH is 8.5. {ECO:0000269|PubMed:2185839};
CC -!- PATHWAY: Purine metabolism; IMP biosynthesis via de novo pathway; N(2)-
CC formyl-N(1)-(5-phospho-D-ribosyl)glycinamide from N(1)-(5-phospho-D-
CC ribosyl)glycinamide (10-formyl THF route): step 1/1.
CC {ECO:0000255|HAMAP-Rule:MF_01930, ECO:0000269|PubMed:8688421}.
CC -!- SUBUNIT: Monomer. Homodimer below pH 6.8. {ECO:0000269|PubMed:10606510,
CC ECO:0000269|PubMed:1522592, ECO:0000269|PubMed:1631098,
CC ECO:0000269|PubMed:2185839, ECO:0000269|PubMed:9698564}.
CC -!- SIMILARITY: Belongs to the GART family. {ECO:0000255|HAMAP-
CC Rule:MF_01930, ECO:0000305}.
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DR EMBL; M13747; AAA83899.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75553.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA16388.1; -; Genomic_DNA.
DR EMBL; AF293167; AAG14584.1; -; Genomic_DNA.
DR PIR; A28486; XYECGF.
DR RefSeq; NP_416995.1; NC_000913.3.
DR RefSeq; WP_001028612.1; NZ_LN832404.1.
DR PDB; 1C2T; X-ray; 2.10 A; A/B=1-212.
DR PDB; 1C3E; X-ray; 2.10 A; A/B=1-209.
DR PDB; 1CDD; X-ray; 2.80 A; A/B=1-212.
DR PDB; 1CDE; X-ray; 2.50 A; A/B/C/D=1-212.
DR PDB; 1GAR; X-ray; 1.96 A; A/B=1-212.
DR PDB; 1GRC; X-ray; 3.00 A; A/B=1-212.
DR PDB; 1JKX; X-ray; 1.60 A; A/B/C/D=1-212.
DR PDB; 2GAR; X-ray; 1.80 A; A=1-212.
DR PDB; 3GAR; X-ray; 1.90 A; A=1-212.
DR PDBsum; 1C2T; -.
DR PDBsum; 1C3E; -.
DR PDBsum; 1CDD; -.
DR PDBsum; 1CDE; -.
DR PDBsum; 1GAR; -.
DR PDBsum; 1GRC; -.
DR PDBsum; 1JKX; -.
DR PDBsum; 2GAR; -.
DR PDBsum; 3GAR; -.
DR AlphaFoldDB; P08179; -.
DR SMR; P08179; -.
DR BioGRID; 4261440; 10.
DR BioGRID; 851312; 1.
DR IntAct; P08179; 1.
DR STRING; 511145.b2500; -.
DR BindingDB; P08179; -.
DR DrugBank; DB04264; (10R)-10-formyl-5,8,10-trideazafolic acid.
DR DrugBank; DB02794; (2S)-2-({4-[(2S)-1-(2-Amino-4-oxo-1,4-dihydro-6-quinazolinyl)-3-{[2-({(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]tetrahydro-2-furanyl}amino)-2-oxoethyl]amino}-2-hydroxy-2-propanyl]benzoyl}ami no)pentanedioic acid.
DR DrugBank; DB02540; 10-formyl-5,8,10-trideazafolic acid.
DR DrugBank; DB02236; Glycinamide Ribonucleotide.
DR jPOST; P08179; -.
DR PaxDb; P08179; -.
DR PRIDE; P08179; -.
DR EnsemblBacteria; AAC75553; AAC75553; b2500.
DR EnsemblBacteria; BAA16388; BAA16388; BAA16388.
DR GeneID; 946973; -.
DR KEGG; ecj:JW2485; -.
DR KEGG; eco:b2500; -.
DR PATRIC; fig|1411691.4.peg.4238; -.
DR EchoBASE; EB0792; -.
DR eggNOG; COG0299; Bacteria.
DR HOGENOM; CLU_038395_1_1_6; -.
DR InParanoid; P08179; -.
DR OMA; TGITIHY; -.
DR PhylomeDB; P08179; -.
DR BioCyc; EcoCyc:GART-MON; -.
DR BioCyc; MetaCyc:GART-MON; -.
DR UniPathway; UPA00074; UER00126.
DR EvolutionaryTrace; P08179; -.
DR PHI-base; PHI:8652; -.
DR PRO; PR:P08179; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0004644; F:phosphoribosylglycinamide formyltransferase activity; IDA:EcoCyc.
DR GO; GO:0006189; P:'de novo' IMP biosynthetic process; IBA:GO_Central.
DR GO; GO:0006974; P:cellular response to DNA damage stimulus; IEP:EcoliWiki.
DR CDD; cd08645; FMT_core_GART; 1.
DR DisProt; DP02740; -.
DR HAMAP; MF_01930; PurN; 1.
DR InterPro; IPR002376; Formyl_transf_N.
DR InterPro; IPR036477; Formyl_transf_N_sf.
DR InterPro; IPR004607; GART.
DR InterPro; IPR001555; GART_AS.
DR Pfam; PF00551; Formyl_trans_N; 1.
DR SUPFAM; SSF53328; SSF53328; 1.
DR TIGRFAMs; TIGR00639; PurN; 1.
DR PROSITE; PS00373; GART; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Purine biosynthesis;
KW Reference proteome; Transferase.
FT CHAIN 1..212
FT /note="Phosphoribosylglycinamide formyltransferase"
FT /id="PRO_0000074943"
FT ACT_SITE 108
FT /note="Proton donor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01930,
FT ECO:0000269|PubMed:10433709"
FT BINDING 11..13
FT /ligand="N(1)-(5-phospho-beta-D-ribosyl)glycinamide"
FT /ligand_id="ChEBI:CHEBI:143788"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01930,
FT ECO:0000269|PubMed:10606510, ECO:0000269|PubMed:1631098"
FT BINDING 64
FT /ligand="(6S)-10-formyltetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57454"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01930,
FT ECO:0000269|PubMed:10606510"
FT BINDING 89..92
FT /ligand="(6S)-10-formyltetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57454"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01930,
FT ECO:0000269|PubMed:10606510, ECO:0000269|PubMed:1631098"
FT BINDING 106
FT /ligand="(6S)-10-formyltetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57454"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01930,
FT ECO:0000269|PubMed:10606510"
FT BINDING 140..144
FT /ligand="(6S)-10-formyltetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57454"
FT /evidence="ECO:0000269|PubMed:10606510,
FT ECO:0000269|PubMed:1631098"
FT BINDING 170..173
FT /ligand="N(1)-(5-phospho-beta-D-ribosyl)glycinamide"
FT /ligand_id="ChEBI:CHEBI:143788"
FT /evidence="ECO:0000269|PubMed:10606510,
FT ECO:0000269|PubMed:1631098"
FT SITE 144
FT /note="Raises pKa of active site His"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01930,
FT ECO:0000269|PubMed:10433709"
FT MUTAGEN 70
FT /note="E->A: Loss of homodimerization. No effect on
FT activity."
FT /evidence="ECO:0000269|PubMed:9698564"
FT MUTAGEN 106
FT /note="N->A,D,G,S: Reduces activity about 2000-fold."
FT /evidence="ECO:0000269|PubMed:8688421"
FT MUTAGEN 106
FT /note="N->E,H,I,K,L,Y: Loss of activity."
FT /evidence="ECO:0000269|PubMed:8688421"
FT MUTAGEN 108
FT /note="H->A,G,M,N,Q,R: Loss of activity."
FT /evidence="ECO:0000269|PubMed:10433709,
FT ECO:0000269|PubMed:8688421"
FT MUTAGEN 108
FT /note="H->E,S,T: Reduces activity about 1000-fold."
FT /evidence="ECO:0000269|PubMed:8688421"
FT MUTAGEN 119
FT /note="H->A: No effect."
FT /evidence="ECO:0000269|PubMed:8688421"
FT MUTAGEN 121
FT /note="H->Q: Increases Km for 5'-phosphoribosylglycinamide
FT 4-fold."
FT /evidence="ECO:0000269|PubMed:10433709"
FT MUTAGEN 135
FT /note="S->A,L: Reduces activity about 1000-fold."
FT /evidence="ECO:0000269|PubMed:8688421"
FT MUTAGEN 137
FT /note="H->F,Q: No effect."
FT /evidence="ECO:0000269|PubMed:8688421"
FT MUTAGEN 144
FT /note="D->A,E,S,Y: Reduces activity about 1000-fold."
FT /evidence="ECO:0000269|PubMed:10433709,
FT ECO:0000269|PubMed:8688421"
FT MUTAGEN 144
FT /note="D->C,F,H,K,L,N,P,Q,R,T,V: Loss of activity."
FT /evidence="ECO:0000269|PubMed:2204419,
FT ECO:0000269|PubMed:8688421"
FT STRAND 2..9
FT /evidence="ECO:0007829|PDB:1JKX"
FT HELIX 12..22
FT /evidence="ECO:0007829|PDB:1JKX"
FT STRAND 25..36
FT /evidence="ECO:0007829|PDB:1JKX"
FT HELIX 41..48
FT /evidence="ECO:0007829|PDB:1JKX"
FT STRAND 52..55
FT /evidence="ECO:0007829|PDB:1JKX"
FT HELIX 58..60
FT /evidence="ECO:0007829|PDB:1JKX"
FT STRAND 61..63
FT /evidence="ECO:0007829|PDB:2GAR"
FT HELIX 64..75
FT /evidence="ECO:0007829|PDB:1JKX"
FT HELIX 76..78
FT /evidence="ECO:0007829|PDB:1JKX"
FT STRAND 81..87
FT /evidence="ECO:0007829|PDB:1JKX"
FT HELIX 94..99
FT /evidence="ECO:0007829|PDB:1JKX"
FT TURN 100..102
FT /evidence="ECO:0007829|PDB:1JKX"
FT STRAND 103..110
FT /evidence="ECO:0007829|PDB:1JKX"
FT STRAND 112..114
FT /evidence="ECO:0007829|PDB:3GAR"
FT HELIX 120..126
FT /evidence="ECO:0007829|PDB:1JKX"
FT STRAND 130..138
FT /evidence="ECO:0007829|PDB:1JKX"
FT STRAND 141..146
FT /evidence="ECO:0007829|PDB:3GAR"
FT STRAND 148..155
FT /evidence="ECO:0007829|PDB:1JKX"
FT HELIX 162..185
FT /evidence="ECO:0007829|PDB:1JKX"
FT STRAND 189..192
FT /evidence="ECO:0007829|PDB:1JKX"
FT STRAND 195..198
FT /evidence="ECO:0007829|PDB:1JKX"
SQ SEQUENCE 212 AA; 23238 MW; D38F326BCBA103FB CRC64;
MNIVVLISGN GSNLQAIIDA CKTNKIKGTV RAVFSNKADA FGLERARQAG IATHTLIASA
FDSREAYDRE LIHEIDMYAP DVVVLAGFMR ILSPAFVSHY AGRLLNIHPS LLPKYPGLHT
HRQALENGDE EHGTSVHFVT DELDGGPVIL QAKVPVFAGD SEDDITARVQ TQEHAIYPLV
ISWFADGRLK MHENAAWLDG QRLPPQGYAA DE
