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Protein

Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnI

Gene

phnI

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Together with PhnG, PhnH and PhnL is required for the transfer of the ribose triphosphate moiety from ATP to methyl phosphonate. PhnI alone has nucleosidase activity, catalyzing the hydrolysis of ATP or GTP forming alpha-D-ribose 5-triphosphate and adenine or guanine, respectively.1 Publication

Catalytic activityi

ATP + methylphosphonate = alpha-D-ribose 1-methylphosphonate 5-triphosphate + adenine.1 Publication
ATP + H2O = adenine + D-ribose 5-triphosphate.1 Publication

Kineticsi

kcat is 1.4 sec(-1) for ATP hydrolysis in the presence of PhnI alone, and 20 sec(-1) for RPnTP synthesis from ATP in the presence of PhnI, PhnG, PhnH and PhnL.

  1. KM=64 µM for GTP (in the presence of PhnI alone)1 Publication
  2. KM=95 µM for ATP (in the presence of PhnI alone)1 Publication
  3. KM=80 µM for GTP (in the presence of PhnI, PhnG, PhnH and PhnL)1 Publication
  4. KM=56 µM for ATP (in the presence of PhnI, PhnG, PhnH and PhnL)1 Publication

    GO - Molecular functioni

    • alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase activity Source: EcoCyc

    GO - Biological processi

    • organic phosphonate catabolic process Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Transferase

    Enzyme and pathway databases

    BioCyciEcoCyc:EG10718-MONOMER.
    ECOL316407:JW4060-MONOMER.
    MetaCyc:EG10718-MONOMER.
    RETL1328306-WGS:GSTH-173-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnI (EC:2.7.8.37)
    Short name:
    RPnTP synthase subunit PhnI
    Alternative name(s):
    Ribose 1-methylphosphonate 5-triphosphate synthase nucleosidase subunit
    Gene namesi
    Name:phnI
    Ordered Locus Names:b4099, JW4060
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10718. phnI.

    Subcellular locationi

    GO - Cellular componenti

    • alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase complex Source: EcoCyc
    Complete GO annotation...

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 354354Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnIPRO_0000058395Add
    BLAST

    Proteomic databases

    PaxDbiP16687.

    Interactioni

    Subunit structurei

    Forms a complex with PhnG, PhnH, PhnJ and PhnK with the suggested composition PhnG4H2I2J2K.1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    phnGP166856EBI-1127704,EBI-9126715

    Protein-protein interaction databases

    BioGridi4263381. 10 interactions.
    DIPiDIP-10488N.
    IntActiP16687. 4 interactions.
    STRINGi511145.b4099.

    Structurei

    Secondary structure

    1
    354
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi2 – 43Combined sources
    Helixi8 – 2417Combined sources
    Helixi34 – 407Combined sources
    Helixi42 – 5211Combined sources
    Helixi57 – 6610Combined sources
    Turni67 – 693Combined sources
    Helixi71 – 8313Combined sources
    Beta strandi87 – 904Combined sources
    Helixi96 – 983Combined sources
    Beta strandi100 – 1056Combined sources
    Beta strandi107 – 1115Combined sources
    Helixi131 – 1344Combined sources
    Helixi155 – 1617Combined sources
    Turni178 – 1803Combined sources
    Helixi189 – 19810Combined sources
    Helixi201 – 21212Combined sources
    Beta strandi221 – 23414Combined sources
    Turni237 – 2393Combined sources
    Beta strandi243 – 26018Combined sources
    Beta strandi263 – 2653Combined sources
    Beta strandi268 – 27912Combined sources
    Helixi282 – 29312Combined sources
    Helixi296 – 2994Combined sources
    Helixi306 – 3083Combined sources
    Helixi310 – 3156Combined sources
    Helixi319 – 3279Combined sources
    Helixi328 – 3303Combined sources
    Helixi334 – 34916Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4XB6X-ray1.70C/G1-354[»]
    ProteinModelPortaliP16687.
    SMRiP16687. Positions 1-353.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the PhnI family.Curated

    Phylogenomic databases

    eggNOGiENOG4105EKV. Bacteria.
    COG3626. LUCA.
    HOGENOMiHOG000127007.
    InParanoidiP16687.
    KOiK06164.
    OMAiIKQARGD.
    OrthoDBiEOG609197.
    PhylomeDBiP16687.

    Family and domain databases

    InterProiIPR008773. PhnI.
    [Graphical view]
    PfamiPF05861. PhnI. 1 hit.
    [Graphical view]
    PIRSFiPIRSF007313. PhnI. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P16687-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MYVAVKGGEK AIDAAHALQE SRRRGDTDLP ELSVAQIEQQ LNLAVDRVMT
    60 70 80 90 100
    EGGIADRELA ALALKQASGD NVEAIFLLRA YRTTLAKLAV SEPLDTTGMR
    110 120 130 140 150
    LERRISAVYK DIPGGQLLGP TYDYTHRLLD FTLLANGEAP TLTTADSEQQ
    160 170 180 190 200
    PSPHVFSLLA RQGLAKFEED SGAQPDDITR TPPVYPCSRS SRLQQLMRGD
    210 220 230 240 250
    EGYLLALAYS TQRGYGRNHP FAGEIRSGYI DVSIVPEELG FAVNVGELLM
    260 270 280 290 300
    TECEMVNGFI DPPGEPPHFT RGYGLVFGMS ERKAMAMALV DRALQAPEYG
    310 320 330 340 350
    EHATGPAQDE EFVLAHADNV EAAGFVSHLK LPHYVDFQAE LELLKRLQQE

    QNHG
    Length:354
    Mass (Da):38,853
    Last modified:November 1, 1991 - v2
    Checksum:i9E974F01B85CCE81
    GO

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti264 – 2641G → D in strain: B.
    Natural varianti351 – 3511Q → K in strain: B.

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    J05260 Genomic DNA. Translation: AAA24347.1.
    D90227 Genomic DNA. Translation: BAA14269.1.
    U14003 Genomic DNA. Translation: AAA96998.1.
    U00096 Genomic DNA. Translation: AAC77060.1.
    AP009048 Genomic DNA. Translation: BAE78102.1.
    PIRiB65219.
    RefSeqiNP_418523.1. NC_000913.3.
    WP_001295388.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC77060; AAC77060; b4099.
    BAE78102; BAE78102; BAE78102.
    GeneIDi948605.
    KEGGiecj:JW4060.
    eco:b4099.
    PATRICi32123757. VBIEscCol129921_4227.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    J05260 Genomic DNA. Translation: AAA24347.1.
    D90227 Genomic DNA. Translation: BAA14269.1.
    U14003 Genomic DNA. Translation: AAA96998.1.
    U00096 Genomic DNA. Translation: AAC77060.1.
    AP009048 Genomic DNA. Translation: BAE78102.1.
    PIRiB65219.
    RefSeqiNP_418523.1. NC_000913.3.
    WP_001295388.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4XB6X-ray1.70C/G1-354[»]
    ProteinModelPortaliP16687.
    SMRiP16687. Positions 1-353.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4263381. 10 interactions.
    DIPiDIP-10488N.
    IntActiP16687. 4 interactions.
    STRINGi511145.b4099.

    Proteomic databases

    PaxDbiP16687.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC77060; AAC77060; b4099.
    BAE78102; BAE78102; BAE78102.
    GeneIDi948605.
    KEGGiecj:JW4060.
    eco:b4099.
    PATRICi32123757. VBIEscCol129921_4227.

    Organism-specific databases

    EchoBASEiEB0712.
    EcoGeneiEG10718. phnI.

    Phylogenomic databases

    eggNOGiENOG4105EKV. Bacteria.
    COG3626. LUCA.
    HOGENOMiHOG000127007.
    InParanoidiP16687.
    KOiK06164.
    OMAiIKQARGD.
    OrthoDBiEOG609197.
    PhylomeDBiP16687.

    Enzyme and pathway databases

    BioCyciEcoCyc:EG10718-MONOMER.
    ECOL316407:JW4060-MONOMER.
    MetaCyc:EG10718-MONOMER.
    RETL1328306-WGS:GSTH-173-MONOMER.

    Miscellaneous databases

    PROiP16687.

    Family and domain databases

    InterProiIPR008773. PhnI.
    [Graphical view]
    PfamiPF05861. PhnI. 1 hit.
    [Graphical view]
    PIRSFiPIRSF007313. PhnI. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Molecular biology of carbon-phosphorus bond cleavage. Cloning and sequencing of the phn (psiD) genes involved in alkylphosphonate uptake and C-P lyase activity in Escherichia coli B."
      Chen C.-M., Ye Q.-Z., Zhu Z., Wanner B.L., Walsh C.T.
      J. Biol. Chem. 265:4461-4471(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: B.
    2. "Molecular analysis of the cryptic and functional phn operons for phosphonate use in Escherichia coli K-12."
      Makino K., Kim S.K., Shinagawa H., Amemura M., Nakata A.
      J. Bacteriol. 173:2665-2672(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    3. "Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes."
      Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.
      Nucleic Acids Res. 23:2105-2119(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    5. "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.
    6. "Intermediates in the transformation of phosphonates to phosphate by bacteria."
      Kamat S.S., Williams H.J., Raushel F.M.
      Nature 480:570-573(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES.
      Strain: K12 / MG1655 / ATCC 47076.
    7. "Five phosphonate operon gene products as components of a multi-subunit complex of the carbon-phosphorus lyase pathway."
      Jochimsen B., Lolle S., McSorley F.R., Nabi M., Stougaard J., Zechel D.L., Hove-Jensen B.
      Proc. Natl. Acad. Sci. U.S.A. 108:11393-11398(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBUNIT.
      Strain: K12.

    Entry informationi

    Entry nameiPHNI_ECOLI
    AccessioniPrimary (citable) accession number: P16687
    Secondary accession number(s): Q2M6K4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1990
    Last sequence update: November 1, 1991
    Last modified: March 16, 2016
    This is version 109 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    The sequence shown is that of strain K12.

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

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

    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 one 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.