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Protein

tRNA dimethylallyltransferase

Gene

miaA

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 dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i6A).2 Publications

Catalytic activityi

Dimethylallyl diphosphate + adenine(37) in tRNA = diphosphate + N(6)-dimethylallyladenine(37) in tRNA.

Cofactori

Mg2+1 Publication

Enzyme regulationi

Strongly inhibited by ADP, ATP and other NTPs.1 Publication

Kineticsi

  1. KM=96 nM for tRNA(Phe)2 Publications
  2. KM=3.2 µM for DMAPP2 Publications

    pH dependencei

    Optimum pH is 6.5-9.2 Publications

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei280 – 2801Required for specificity towards tRNA substrates containing a purine at position 29

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi17 – 248ATPSequence analysis

    GO - Molecular functioni

    • ATP binding Source: UniProtKB-HAMAP
    • tRNA dimethylallyltransferase activity Source: EcoCyc

    GO - Biological processi

    • cellular response to heat Source: EcoCyc
    • tRNA modification Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Transferase

    Keywords - Biological processi

    tRNA processing

    Keywords - Ligandi

    ATP-binding, Magnesium, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:EG10595-MONOMER.
    ECOL316407:JW4129-MONOMER.
    MetaCyc:EG10595-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    tRNA dimethylallyltransferase (EC:2.5.1.75)
    Alternative name(s):
    Dimethylallyl diphosphate:tRNA dimethylallyltransferase
    Short name:
    DMAPP:tRNA dimethylallyltransferase
    Short name:
    DMATase
    Isopentenyl-diphosphate:tRNA isopentenyltransferase
    Short name:
    IPP transferase
    Short name:
    IPPT
    Short name:
    IPTase
    Gene namesi
    Name:miaA
    Synonyms:trpX
    Ordered Locus Names:b4171, JW4129
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10595. miaA.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 316316tRNA dimethylallyltransferasePRO_0000163913Add
    BLAST

    Proteomic databases

    PaxDbiP16384.
    PRIDEiP16384.

    Expressioni

    Inductioni

    By 2-aminopurine.

    Interactioni

    Subunit structurei

    Monomer. Binds to tRNA(Phe).3 Publications

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei108 – 1081Interaction with substrate tRNA
    Sitei130 – 1301Interaction with substrate tRNA

    Protein-protein interaction databases

    BioGridi4263002. 39 interactions.
    IntActiP16384. 5 interactions.
    STRINGi511145.b4171.

    Structurei

    Secondary structure

    1
    316
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi11 – 166Combined sources
    Helixi23 – 3311Combined sources
    Beta strandi36 – 405Combined sources
    Turni43 – 464Combined sources
    Turni52 – 554Combined sources
    Helixi59 – 646Combined sources
    Beta strandi67 – 715Combined sources
    Helixi81 – 9717Combined sources
    Beta strandi101 – 1077Combined sources
    Helixi109 – 1168Combined sources
    Helixi127 – 15226Combined sources
    Helixi154 – 1596Combined sources
    Helixi165 – 17814Combined sources
    Helixi182 – 1865Combined sources
    Beta strandi194 – 20310Combined sources
    Helixi207 – 22317Combined sources
    Helixi226 – 23611Combined sources
    Turni244 – 2474Combined sources
    Helixi251 – 2599Combined sources
    Helixi264 – 28724Combined sources
    Beta strandi293 – 2964Combined sources
    Helixi300 – 3089Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2ZM5X-ray2.55A/B1-316[»]
    2ZXUX-ray2.75A/B1-316[»]
    3FOZX-ray2.50A/B1-316[»]
    ProteinModelPortaliP16384.
    SMRiP16384. Positions 7-311.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP16384.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni19 – 246Substrate bindingBy similarity
    Regioni42 – 454Interaction with substrate tRNA
    Regioni120 – 1245Interaction with substrate tRNA
    Regioni166 – 1705Interaction with substrate tRNA
    Regioni206 – 22924Interaction with isopentenylpyrophosphate transferaseAdd
    BLAST
    Regioni247 – 2526Interaction with substrate tRNA
    Regioni280 – 2878Interaction with substrate tRNA

    Sequence similaritiesi

    Belongs to the IPP transferase family.Curated

    Phylogenomic databases

    eggNOGiENOG4105DKX. Bacteria.
    COG0324. LUCA.
    HOGENOMiHOG000039996.
    InParanoidiP16384.
    KOiK00791.
    OMAiHTRNYAK.
    PhylomeDBiP16384.

    Family and domain databases

    Gene3Di3.40.50.300. 1 hit.
    HAMAPiMF_00185. IPP_trans. 1 hit.
    InterProiIPR018022. IPP_trans.
    IPR027417. P-loop_NTPase.
    [Graphical view]
    PfamiPF01715. IPPT. 1 hit.
    [Graphical view]
    SUPFAMiSSF52540. SSF52540. 1 hit.
    TIGRFAMsiTIGR00174. miaA. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P16384-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSDISKASLP KAIFLMGPTA SGKTALAIEL RKILPVELIS VDSALIYKGM
    60 70 80 90 100
    DIGTAKPNAE ELLAAPHRLL DIRDPSQAYS AADFRRDALA EMADITAAGR
    110 120 130 140 150
    IPLLVGGTML YFKALLEGLS PLPSADPEVR ARIEQQAAEQ GWESLHRQLQ
    160 170 180 190 200
    EVDPVAAARI HPNDPQRLSR ALEVFFISGK TLTELTQTSG DALPYQVHQF
    210 220 230 240 250
    AIAPASRELL HQRIEQRFHQ MLASGFEAEV RALFARGDLH TDLPSIRCVG
    260 270 280 290 300
    YRQMWSYLEG EISYDEMVYR GVCATRQLAK RQITWLRGWE GVHWLDSEKP
    310
    EQARDEVLQV VGAIAG
    Length:316
    Mass (Da):35,065
    Last modified:November 1, 1991 - v2
    Checksum:iFBFDC18770781C8F
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti101 – 1011I → D in AAC43396 (Ref. 7) Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M63655 Genomic DNA. Translation: AAA24174.1.
    U14003 Genomic DNA. Translation: AAA97067.1.
    U00096 Genomic DNA. Translation: AAC77128.1.
    AP009048 Genomic DNA. Translation: BAE78172.1.
    D00743 Genomic DNA. Translation: BAA00643.1.
    U00005 Unassigned DNA. Translation: AAC43396.1.
    Z11831 Genomic DNA. Translation: CAA77852.1.
    PIRiB37318.
    RefSeqiNP_418592.1. NC_000913.3.
    WP_001280345.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC77128; AAC77128; b4171.
    BAE78172; BAE78172; BAE78172.
    GeneIDi948690.
    KEGGiecj:JW4129.
    eco:b4171.
    PATRICi32123915. VBIEscCol129921_4302.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M63655 Genomic DNA. Translation: AAA24174.1.
    U14003 Genomic DNA. Translation: AAA97067.1.
    U00096 Genomic DNA. Translation: AAC77128.1.
    AP009048 Genomic DNA. Translation: BAE78172.1.
    D00743 Genomic DNA. Translation: BAA00643.1.
    U00005 Unassigned DNA. Translation: AAC43396.1.
    Z11831 Genomic DNA. Translation: CAA77852.1.
    PIRiB37318.
    RefSeqiNP_418592.1. NC_000913.3.
    WP_001280345.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2ZM5X-ray2.55A/B1-316[»]
    2ZXUX-ray2.75A/B1-316[»]
    3FOZX-ray2.50A/B1-316[»]
    ProteinModelPortaliP16384.
    SMRiP16384. Positions 7-311.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4263002. 39 interactions.
    IntActiP16384. 5 interactions.
    STRINGi511145.b4171.

    Proteomic databases

    PaxDbiP16384.
    PRIDEiP16384.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC77128; AAC77128; b4171.
    BAE78172; BAE78172; BAE78172.
    GeneIDi948690.
    KEGGiecj:JW4129.
    eco:b4171.
    PATRICi32123915. VBIEscCol129921_4302.

    Organism-specific databases

    EchoBASEiEB0590.
    EcoGeneiEG10595. miaA.

    Phylogenomic databases

    eggNOGiENOG4105DKX. Bacteria.
    COG0324. LUCA.
    HOGENOMiHOG000039996.
    InParanoidiP16384.
    KOiK00791.
    OMAiHTRNYAK.
    PhylomeDBiP16384.

    Enzyme and pathway databases

    BioCyciEcoCyc:EG10595-MONOMER.
    ECOL316407:JW4129-MONOMER.
    MetaCyc:EG10595-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiP16384.
    PROiP16384.

    Family and domain databases

    Gene3Di3.40.50.300. 1 hit.
    HAMAPiMF_00185. IPP_trans. 1 hit.
    InterProiIPR018022. IPP_trans.
    IPR027417. P-loop_NTPase.
    [Graphical view]
    PfamiPF01715. IPPT. 1 hit.
    [Graphical view]
    SUPFAMiSSF52540. SSF52540. 1 hit.
    TIGRFAMsiTIGR00174. miaA. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiMIAA_ECOLI
    AccessioniPrimary (citable) accession number: P16384
    Secondary accession number(s): Q2M6D4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1990
    Last sequence update: November 1, 1991
    Last modified: September 7, 2016
    This is version 142 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Specific tRNA undermodification may be a switch to higher mutation frequency when cells are subject to environmental stresses other than treatment with mutagens.

    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.