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Protein

Phosphoribosylglycinamide formyltransferase

Gene

purN

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the transfer of a formyl group from 10-formyltetrahydrofolate to 5-phospho-ribosyl-glycinamide (GAR), producing 5-phospho-ribosyl-N-formylglycinamide (FGAR) and tetrahydrofolate.UniRule annotation2 Publications

Catalytic activityi

10-formyltetrahydrofolate + N(1)-(5-phospho-D-ribosyl)glycinamide = tetrahydrofolate + N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide.UniRule annotation2 Publications

Enzyme regulationi

Inhibited by N10-(bromoacetyl)-5,8-dideazafolate.1 Publication

Kineticsi

kcat is 20.7 sec(-1) for (6R)-N10-formyltetrahydrofolate (at pH 8.5). kcat is 13.5 sec(-1) for (6R)-N10-formyltetrahydrofolate (at pH 7.5).1 Publication

  1. KM=77.5 µM for (6R)-N10-formyltetrahydrofolate (at pH 8.5)1 Publication
  2. KM=84.8 µM for (6R)-N10-formyltetrahydrofolate (at pH 7.5)1 Publication

    pH dependencei

    Optimum pH is 8.5.1 Publication

    Pathway:iIMP biosynthesis via de novo pathway

    This protein is involved in step 1 of the subpathway that synthesizes N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide from N(1)-(5-phospho-D-ribosyl)glycinamide (10-formyl THF route).UniRule annotation1 Publication
    Proteins known to be involved in this subpathway in this organism are:
    1. Phosphoribosylglycinamide formyltransferase (purN)
    This subpathway is part of the pathway IMP biosynthesis via de novo pathway, which is itself part of Purine metabolism.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide from N(1)-(5-phospho-D-ribosyl)glycinamide (10-formyl THF route), the pathway IMP biosynthesis via de novo pathway and in Purine metabolism.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei64 – 64110-formyltetrahydrofolateUniRule annotation1 Publication
    Binding sitei106 – 106110-formyltetrahydrofolateUniRule annotation1 Publication
    Active sitei108 – 1081Proton donorUniRule annotation1 Publication
    Sitei144 – 1441Raises pKa of active site HisUniRule annotation1 Publication

    GO - Molecular functioni

    GO - Biological processi

    • 'de novo' IMP biosynthetic process Source: UniProtKB-HAMAP
    • cellular response to DNA damage stimulus Source: EcoliWiki
    Complete GO annotation...

    Keywords - Molecular functioni

    Transferase

    Keywords - Biological processi

    Purine biosynthesis

    Enzyme and pathway databases

    BioCyciEcoCyc:GART-MONOMER.
    ECOL316407:JW2485-MONOMER.
    MetaCyc:GART-MONOMER.
    RETL1328306-WGS:GSTH-1500-MONOMER.
    UniPathwayiUPA00074; UER00126.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Phosphoribosylglycinamide formyltransferaseUniRule annotation (EC:2.1.2.2UniRule annotation2 Publications)
    Alternative name(s):
    5'-phosphoribosylglycinamide transformylaseUniRule annotation
    GAR transformylaseUniRule annotation
    Short name:
    GARTUniRule annotation
    Gene namesi
    Name:purN1 PublicationUniRule annotation
    Ordered Locus Names:b2500, JW2485
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10799. purN.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi70 – 701E → A: Loss of homodimerization. No effect on activity. 1 Publication
    Mutagenesisi106 – 1061N → A, D, G or S: Reduces activity about 2000-fold. 1 Publication
    Mutagenesisi106 – 1061N → E, H, I, K, L or Y: Loss of activity. 1 Publication
    Mutagenesisi108 – 1081H → A, G, M, N, Q or R: Loss of activity. 2 Publications
    Mutagenesisi108 – 1081H → E, S or T: Reduces activity about 1000-fold. 1 Publication
    Mutagenesisi119 – 1191H → A: No effect. 1 Publication
    Mutagenesisi121 – 1211H → Q: Increases Km for 5'-phosphoribosylglycinamide 4-fold. 1 Publication
    Mutagenesisi135 – 1351S → A or L: Reduces activity about 1000-fold. 1 Publication
    Mutagenesisi137 – 1371H → F or Q: No effect. 1 Publication
    Mutagenesisi144 – 1441D → A, E, S or Y: Reduces activity about 1000-fold. 2 Publications
    Mutagenesisi144 – 1441D → C, F, H, K, L, N, P, Q, R, T or V: Loss of activity. 2 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 212212Phosphoribosylglycinamide formyltransferasePRO_0000074943Add
    BLAST

    Proteomic databases

    PaxDbiP08179.
    PRIDEiP08179.

    Interactioni

    Subunit structurei

    Monomer. Homodimer below pH 6.8.5 Publications

    Protein-protein interaction databases

    IntActiP08179. 1 interaction.
    STRINGi511145.b2500.

    Structurei

    Secondary structure

    1
    212
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi2 – 98Combined sources
    Helixi12 – 2211Combined sources
    Beta strandi25 – 3612Combined sources
    Helixi41 – 488Combined sources
    Beta strandi52 – 554Combined sources
    Helixi58 – 603Combined sources
    Beta strandi61 – 633Combined sources
    Helixi64 – 7512Combined sources
    Helixi76 – 783Combined sources
    Beta strandi81 – 877Combined sources
    Helixi94 – 996Combined sources
    Turni100 – 1023Combined sources
    Beta strandi103 – 1108Combined sources
    Beta strandi112 – 1143Combined sources
    Helixi120 – 1267Combined sources
    Beta strandi130 – 1389Combined sources
    Beta strandi141 – 1466Combined sources
    Beta strandi148 – 1558Combined sources
    Helixi162 – 18524Combined sources
    Beta strandi189 – 1924Combined sources
    Beta strandi195 – 1984Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1C2TX-ray2.10A/B1-212[»]
    1C3EX-ray2.10A/B1-209[»]
    1CDDX-ray2.80A/B1-212[»]
    1CDEX-ray2.50A/B/C/D1-212[»]
    1GARX-ray1.96A/B1-212[»]
    1GRCX-ray3.00A/B1-212[»]
    1JKXX-ray1.60A/B/C/D1-212[»]
    2GARX-ray1.80A1-212[»]
    3GARX-ray1.90A1-212[»]
    ProteinModelPortaliP08179.
    SMRiP08179. Positions 1-209.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP08179.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni11 – 1335'-phosphoribosylglycinamide bindingUniRule annotation2 Publications
    Regioni89 – 92410-formyltetrahydrofolate bindingUniRule annotation2 Publications
    Regioni140 – 144510-formyltetrahydrofolate binding2 Publications
    Regioni170 – 17345'-phosphoribosylglycinamide binding2 Publications

    Sequence similaritiesi

    Belongs to the GART family.UniRule annotationCurated

    Phylogenomic databases

    eggNOGiCOG0299.
    HOGENOMiHOG000033575.
    InParanoidiP08179.
    KOiK11175.
    OMAiEYDTGRI.
    OrthoDBiEOG615VP4.
    PhylomeDBiP08179.

    Family and domain databases

    Gene3Di3.40.50.170. 1 hit.
    HAMAPiMF_01930. PurN.
    InterProiIPR002376. Formyl_transf_N.
    IPR001555. GART_AS.
    IPR004607. PurN_trans.
    [Graphical view]
    PfamiPF00551. Formyl_trans_N. 1 hit.
    [Graphical view]
    SUPFAMiSSF53328. SSF53328. 1 hit.
    TIGRFAMsiTIGR00639. PurN. 1 hit.
    PROSITEiPS00373. GART. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P08179-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MNIVVLISGN GSNLQAIIDA CKTNKIKGTV RAVFSNKADA FGLERARQAG
    60 70 80 90 100
    IATHTLIASA FDSREAYDRE LIHEIDMYAP DVVVLAGFMR ILSPAFVSHY
    110 120 130 140 150
    AGRLLNIHPS LLPKYPGLHT HRQALENGDE EHGTSVHFVT DELDGGPVIL
    160 170 180 190 200
    QAKVPVFAGD SEDDITARVQ TQEHAIYPLV ISWFADGRLK MHENAAWLDG
    210
    QRLPPQGYAA DE
    Length:212
    Mass (Da):23,238
    Last modified:August 1, 1988 - v1
    Checksum:iD38F326BCBA103FB
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M13747 Genomic DNA. Translation: AAA83899.1.
    U00096 Genomic DNA. Translation: AAC75553.1.
    AP009048 Genomic DNA. Translation: BAA16388.1.
    AF293167 Genomic DNA. Translation: AAG14584.1.
    PIRiA28486. XYECGF.
    RefSeqiNP_416995.1. NC_000913.3.
    WP_001028612.1. NZ_CP010445.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75553; AAC75553; b2500.
    BAA16388; BAA16388; BAA16388.
    GeneIDi946973.
    KEGGieco:b2500.
    PATRICi32120389. VBIEscCol129921_2597.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M13747 Genomic DNA. Translation: AAA83899.1.
    U00096 Genomic DNA. Translation: AAC75553.1.
    AP009048 Genomic DNA. Translation: BAA16388.1.
    AF293167 Genomic DNA. Translation: AAG14584.1.
    PIRiA28486. XYECGF.
    RefSeqiNP_416995.1. NC_000913.3.
    WP_001028612.1. NZ_CP010445.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1C2TX-ray2.10A/B1-212[»]
    1C3EX-ray2.10A/B1-209[»]
    1CDDX-ray2.80A/B1-212[»]
    1CDEX-ray2.50A/B/C/D1-212[»]
    1GARX-ray1.96A/B1-212[»]
    1GRCX-ray3.00A/B1-212[»]
    1JKXX-ray1.60A/B/C/D1-212[»]
    2GARX-ray1.80A1-212[»]
    3GARX-ray1.90A1-212[»]
    ProteinModelPortaliP08179.
    SMRiP08179. Positions 1-209.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    IntActiP08179. 1 interaction.
    STRINGi511145.b2500.

    Chemistry

    BindingDBiP08179.

    Proteomic databases

    PaxDbiP08179.
    PRIDEiP08179.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC75553; AAC75553; b2500.
    BAA16388; BAA16388; BAA16388.
    GeneIDi946973.
    KEGGieco:b2500.
    PATRICi32120389. VBIEscCol129921_2597.

    Organism-specific databases

    EchoBASEiEB0792.
    EcoGeneiEG10799. purN.

    Phylogenomic databases

    eggNOGiCOG0299.
    HOGENOMiHOG000033575.
    InParanoidiP08179.
    KOiK11175.
    OMAiEYDTGRI.
    OrthoDBiEOG615VP4.
    PhylomeDBiP08179.

    Enzyme and pathway databases

    UniPathwayiUPA00074; UER00126.
    BioCyciEcoCyc:GART-MONOMER.
    ECOL316407:JW2485-MONOMER.
    MetaCyc:GART-MONOMER.
    RETL1328306-WGS:GSTH-1500-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiP08179.
    PROiP08179.

    Family and domain databases

    Gene3Di3.40.50.170. 1 hit.
    HAMAPiMF_01930. PurN.
    InterProiIPR002376. Formyl_transf_N.
    IPR001555. GART_AS.
    IPR004607. PurN_trans.
    [Graphical view]
    PfamiPF00551. Formyl_trans_N. 1 hit.
    [Graphical view]
    SUPFAMiSSF53328. SSF53328. 1 hit.
    TIGRFAMsiTIGR00639. PurN. 1 hit.
    PROSITEiPS00373. GART. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Identification and nucleotide sequence of a gene encoding 5'-phosphoribosylglycinamide transformylase in Escherichia coli K12."
      Smith J.M., Daum H.A. III
      J. Biol. Chem. 262:10565-10569(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    2. "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features."
      Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T.
      , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.
      DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    5. "Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics."
      Pupo G.M., Lan R., Reeves P.R.
      Proc. Natl. Acad. Sci. U.S.A. 97:10567-10572(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ECOR 7.
    6. "Subcloning, characterization, and affinity labeling of Escherichia coli glycinamide ribonucleotide transformylase."
      Inglese J., Johnson D.L., Shiau A., Smith J.M., Benkovic S.J.
      Biochemistry 29:1436-1443(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 1-6, FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
    7. "N10-Formyltetrahydrofolate is the formyl donor for glycinamide ribotide transformylase in Escherichia coli."
      Dev I.K., Harvey R.J.
      J. Biol. Chem. 253:4242-4244(1978) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY.
    8. "Active-site mapping and site-specific mutagenesis of glycinamide ribonucleotide transformylase from Escherichia coli."
      Inglese J., Smith J.M., Benkovic S.J.
      Biochemistry 29:6678-6687(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF ASP-144, PARTIAL PROTEIN SEQUENCE.
    9. "A rapid screen of active site mutants in glycinamide ribonucleotide transformylase."
      Warren M.S., Marolewski A.E., Benkovic S.J.
      Biochemistry 35:8855-8862(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF ASN-106; HIS-108; HIS-119; SER-135; HIS-137 AND ASP-144, PATHWAY.
    10. "Catalytic mechanism of Escherichia coli glycinamide ribonucleotide transformylase probed by site-directed mutagenesis and pH-dependent studies."
      Shim J.H., Benkovic S.J.
      Biochemistry 38:10024-10031(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF HIS-108; HIS-121 AND ASP-144, ACTIVE SITE.
    11. "Crystal structure of glycinamide ribonucleotide transformylase from Escherichia coli at 3.0-A resolution. A target enzyme for chemotherapy."
      Chen P., Schulze-Gahmen U., Stura E.A., Inglese J., Johnson D.L., Marolewski A., Benkovic S.J., Wilson I.A.
      J. Mol. Biol. 227:283-292(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG.
    12. "Structures of apo and complexed Escherichia coli glycinamide ribonucleotide transformylase."
      Almassy R.J., Janson C.A., Kan C.-C., Hostomska Z.
      Proc. Natl. Acad. Sci. U.S.A. 89:6114-6118(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS.
    13. "A pH-dependent stabilization of an active site loop observed from low and high pH crystal structures of mutant monomeric glycinamide ribonucleotide transformylase at 1.8 to 1.9 A."
      Su Y., Yamashita M.M., Greasley S.E., Mullen C.A., Shim J.H., Jennings P.A., Benkovic S.J., Wilson I.A.
      J. Mol. Biol. 281:485-499(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF MUTANT ALA-70 IN COMPLEX WITH SUBSTRATE ANALOGS, SUBUNIT.
    14. "New insights into inhibitor design from the crystal structure and NMR studies of Escherichia coli GAR transformylase in complex with beta-GAR and 10-formyl-5,8,10-trideazafolic acid."
      Greasley S.E., Yamashita M.M., Cai H., Benkovic S.J., Boger D.L., Wilson I.A.
      Biochemistry 38:16783-16793(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS.

    Entry informationi

    Entry nameiPUR3_ECOLI
    AccessioniPrimary (citable) accession number: P08179
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1988
    Last sequence update: August 1, 1988
    Last modified: July 22, 2015
    This is version 146 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.