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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.

    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    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)DescriptionActionsGraphical viewLength
    ChainiPRO_00000583951 – 354Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnIAdd BLAST354

    Proteomic databases

    PaxDbiP16687.
    PRIDEiP16687.

    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 interactors.
    DIPiDIP-10488N.
    IntActiP16687. 4 interactors.
    STRINGi511145.b4099.

    Structurei

    Secondary structure

    1354
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi2 – 4Combined sources3
    Helixi8 – 24Combined sources17
    Helixi34 – 40Combined sources7
    Helixi42 – 52Combined sources11
    Helixi57 – 66Combined sources10
    Turni67 – 69Combined sources3
    Helixi71 – 83Combined sources13
    Beta strandi87 – 90Combined sources4
    Helixi96 – 98Combined sources3
    Beta strandi100 – 105Combined sources6
    Beta strandi107 – 111Combined sources5
    Helixi131 – 134Combined sources4
    Helixi155 – 161Combined sources7
    Turni178 – 180Combined sources3
    Helixi189 – 198Combined sources10
    Helixi201 – 212Combined sources12
    Beta strandi221 – 234Combined sources14
    Turni237 – 239Combined sources3
    Beta strandi243 – 260Combined sources18
    Beta strandi263 – 265Combined sources3
    Beta strandi268 – 279Combined sources12
    Helixi282 – 293Combined sources12
    Helixi296 – 299Combined sources4
    Helixi306 – 308Combined sources3
    Helixi310 – 315Combined sources6
    Helixi319 – 327Combined sources9
    Helixi328 – 330Combined sources3
    Helixi334 – 349Combined sources16

    3D structure databases

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

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the PhnI family.Curated

    Phylogenomic databases

    eggNOGiENOG4105EKV. Bacteria.
    COG3626. LUCA.
    HOGENOMiHOG000127007.
    InParanoidiP16687.
    KOiK06164.
    OMAiIKQARGD.
    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)DescriptionActionsGraphical viewLength
    Natural varianti264G → D in strain: B. 1
    Natural varianti351Q → K in strain: B. 1

    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
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    4XB6X-ray1.70C/G1-354[»]
    ProteinModelPortaliP16687.
    SMRiP16687.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

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

    Proteomic databases

    PaxDbiP16687.
    PRIDEiP16687.

    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.
    PhylomeDBiP16687.

    Enzyme and pathway databases

    BioCyciEcoCyc:EG10718-MONOMER.
    ECOL316407:JW4060-MONOMER.
    MetaCyc:EG10718-MONOMER.

    Miscellaneous databases

    PROiP16687.

    Family and domain databases

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

    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: November 2, 2016
    This is version 112 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.