MIAA_ECOLI
ID MIAA_ECOLI Reviewed; 316 AA.
AC P16384; Q2M6D4;
DT 01-AUG-1990, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1991, sequence version 2.
DT 03-AUG-2022, entry version 178.
DE RecName: Full=tRNA dimethylallyltransferase;
DE EC=2.5.1.75;
DE AltName: Full=Dimethylallyl diphosphate:tRNA dimethylallyltransferase;
DE Short=DMAPP:tRNA dimethylallyltransferase;
DE Short=DMATase;
DE AltName: Full=Isopentenyl-diphosphate:tRNA isopentenyltransferase;
DE Short=IPP transferase;
DE Short=IPPT;
DE Short=IPTase;
GN Name=miaA; Synonyms=trpX; OrderedLocusNames=b4171, JW4129;
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=1999389; DOI=10.1128/jb.173.5.1711-1721.1991;
RA Winkler M.E., Connolly D.M.;
RT "Structure of Escherichia coli K-12 miaA and characterization of the
RT mutator phenotype caused by miaA insertion mutations.";
RL J. Bacteriol. 173:1711-1721(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=7610040; DOI=10.1093/nar/23.12.2105;
RA Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.;
RT "Analysis of the Escherichia coli genome VI: DNA sequence of the region
RT from 92.8 through 100 minutes.";
RL Nucleic Acids Res. 23:2105-2119(1995).
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] OF 109-170.
RC STRAIN=K12;
RX PubMed=2656644; DOI=10.1128/jb.171.6.3233-3246.1989;
RA Connolly D.M., Winkler M.E.;
RT "Genetic and physiological relationships among the miaA gene, 2-methylthio-
RT N6-(delta 2-isopentenyl)-adenosine tRNA modification, and spontaneous
RT mutagenesis in Escherichia coli K-12.";
RL J. Bacteriol. 171:3233-3246(1989).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 101-316.
RX PubMed=2020545; DOI=10.1093/nar/19.5.1063;
RA Kajitani M., Ishihama A.;
RT "Identification and sequence determination of the host factor gene for
RT bacteriophage Q beta.";
RL Nucleic Acids Res. 19:1063-1066(1991).
RN [7]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 101-316.
RC STRAIN=K12;
RA Noble J.A., Innis M.A., Banuett F., Herskowitz I.;
RL Submitted (MAY-1993) to the EMBL/GenBank/DDBJ databases.
RN [8]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-65.
RC STRAIN=K12;
RX PubMed=1594459; DOI=10.1093/nar/20.9.2379;
RA Tsui H.-C.T., Mandavilli B.S., Winkler M.E.;
RT "Nonconserved segment of the MutL protein from Escherichia coli K-12 and
RT Salmonella typhimurium.";
RL Nucleic Acids Res. 20:2379-2379(1992).
RN [9]
RP FUNCTION, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RX PubMed=9012675; DOI=10.1021/bi962225l;
RA Moore J.A., Poulter C.D.;
RT "Escherichia coli dimethylallyl diphosphate:tRNA dimethylallyltransferase:
RT a binding mechanism for recombinant enzyme.";
RL Biochemistry 36:604-614(1997).
RN [10]
RP FUNCTION, ACTIVITY REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RX PubMed=9148919; DOI=10.1074/jbc.272.20.13073;
RA Leung H.-C.E., Chen Y., Winkler M.E.;
RT "Regulation of substrate recognition by the MiaA tRNA prenyltransferase
RT modification enzyme of Escherichia coli K-12.";
RL J. Biol. Chem. 272:13073-13083(1997).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH TRNA(PHE).
RX PubMed=19158097; DOI=10.1074/jbc.c800235200;
RA Seif E., Hallberg B.M.;
RT "RNA-protein mutually induced fit: structure of Escherichia coli
RT isopentenyl-tRNA transferase in complex with tRNA(Phe).";
RL J. Biol. Chem. 284:6600-6604(2009).
CC -!- FUNCTION: Catalyzes the transfer of a dimethylallyl group onto the
CC adenine at position 37 in tRNAs that read codons beginning with
CC uridine, leading to the formation of N6-(dimethylallyl)adenosine
CC (i(6)A). {ECO:0000269|PubMed:9012675, ECO:0000269|PubMed:9148919}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=adenosine(37) in tRNA + dimethylallyl diphosphate =
CC diphosphate + N(6)-dimethylallyladenosine(37) in tRNA;
CC Xref=Rhea:RHEA:26482, Rhea:RHEA-COMP:10162, Rhea:RHEA-COMP:10375,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:57623, ChEBI:CHEBI:74411,
CC ChEBI:CHEBI:74415; EC=2.5.1.75;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:9012675};
CC -!- ACTIVITY REGULATION: Strongly inhibited by ADP, ATP and other NTPs.
CC {ECO:0000269|PubMed:9148919}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=96 nM for tRNA(Phe) {ECO:0000269|PubMed:9012675,
CC ECO:0000269|PubMed:9148919};
CC KM=3.2 uM for DMAPP {ECO:0000269|PubMed:9012675,
CC ECO:0000269|PubMed:9148919};
CC pH dependence:
CC Optimum pH is 6.5-9. {ECO:0000269|PubMed:9012675,
CC ECO:0000269|PubMed:9148919};
CC -!- SUBUNIT: Monomer. Binds to tRNA(Phe). {ECO:0000269|PubMed:19158097,
CC ECO:0000269|PubMed:9012675, ECO:0000269|PubMed:9148919}.
CC -!- INDUCTION: By 2-aminopurine.
CC -!- MISCELLANEOUS: Specific tRNA undermodification may be a switch to
CC higher mutation frequency when cells are subject to environmental
CC stresses other than treatment with mutagens.
CC -!- SIMILARITY: Belongs to the IPP transferase family. {ECO:0000305}.
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DR EMBL; M63655; AAA24174.1; -; Genomic_DNA.
DR EMBL; U14003; AAA97067.1; -; Genomic_DNA.
DR EMBL; U00096; AAC77128.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE78172.1; -; Genomic_DNA.
DR EMBL; D00743; BAA00643.1; -; Genomic_DNA.
DR EMBL; U00005; AAC43396.1; -; Unassigned_DNA.
DR EMBL; Z11831; CAA77852.1; -; Genomic_DNA.
DR PIR; B37318; B37318.
DR RefSeq; NP_418592.1; NC_000913.3.
DR RefSeq; WP_001280345.1; NZ_STEB01000013.1.
DR PDB; 2ZM5; X-ray; 2.55 A; A/B=1-316.
DR PDB; 2ZXU; X-ray; 2.75 A; A/B=1-316.
DR PDB; 3FOZ; X-ray; 2.50 A; A/B=1-316.
DR PDBsum; 2ZM5; -.
DR PDBsum; 2ZXU; -.
DR PDBsum; 3FOZ; -.
DR AlphaFoldDB; P16384; -.
DR SMR; P16384; -.
DR BioGRID; 4263002; 83.
DR BioGRID; 852982; 2.
DR IntAct; P16384; 5.
DR STRING; 511145.b4171; -.
DR DrugBank; DB02270; Dimethylallyl S-Thiolodiphosphate.
DR jPOST; P16384; -.
DR PaxDb; P16384; -.
DR PRIDE; P16384; -.
DR EnsemblBacteria; AAC77128; AAC77128; b4171.
DR EnsemblBacteria; BAE78172; BAE78172; BAE78172.
DR GeneID; 66671916; -.
DR GeneID; 948690; -.
DR KEGG; ecj:JW4129; -.
DR KEGG; eco:b4171; -.
DR PATRIC; fig|1411691.4.peg.2530; -.
DR EchoBASE; EB0590; -.
DR eggNOG; COG0324; Bacteria.
DR HOGENOM; CLU_032616_0_0_6; -.
DR InParanoid; P16384; -.
DR OMA; YAKRQYT; -.
DR PhylomeDB; P16384; -.
DR BioCyc; EcoCyc:EG10595-MON; -.
DR BioCyc; MetaCyc:EG10595-MON; -.
DR EvolutionaryTrace; P16384; -.
DR PRO; PR:P16384; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0052381; F:tRNA dimethylallyltransferase activity; IDA:EcoCyc.
DR GO; GO:0034605; P:cellular response to heat; IMP:EcoCyc.
DR GO; GO:1990497; P:regulation of cytoplasmic translation in response to stress; IMP:EcoCyc.
DR GO; GO:0006400; P:tRNA modification; IMP:EcoCyc.
DR Gene3D; 3.40.50.300; -; 1.
DR HAMAP; MF_00185; IPP_trans; 1.
DR InterPro; IPR039657; Dimethylallyltransferase.
DR InterPro; IPR018022; IPT.
DR InterPro; IPR027417; P-loop_NTPase.
DR PANTHER; PTHR11088; PTHR11088; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR TIGRFAMs; TIGR00174; miaA; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Magnesium; Nucleotide-binding;
KW Reference proteome; Transferase; tRNA processing.
FT CHAIN 1..316
FT /note="tRNA dimethylallyltransferase"
FT /id="PRO_0000163913"
FT REGION 42..45
FT /note="Interaction with substrate tRNA"
FT REGION 120..124
FT /note="Interaction with substrate tRNA"
FT REGION 166..170
FT /note="Interaction with substrate tRNA"
FT REGION 206..229
FT /note="Interaction with isopentenylpyrophosphate
FT transferase"
FT REGION 247..252
FT /note="Interaction with substrate tRNA"
FT REGION 280..287
FT /note="Interaction with substrate tRNA"
FT BINDING 17..24
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255"
FT BINDING 19..24
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT SITE 108
FT /note="Interaction with substrate tRNA"
FT SITE 130
FT /note="Interaction with substrate tRNA"
FT SITE 280
FT /note="Required for specificity towards tRNA substrates
FT containing a purine at position 29"
FT CONFLICT 101
FT /note="I -> D (in Ref. 7; AAC43396)"
FT /evidence="ECO:0000305"
FT STRAND 11..16
FT /evidence="ECO:0007829|PDB:3FOZ"
FT HELIX 23..33
FT /evidence="ECO:0007829|PDB:3FOZ"
FT STRAND 36..40
FT /evidence="ECO:0007829|PDB:3FOZ"
FT TURN 43..46
FT /evidence="ECO:0007829|PDB:3FOZ"
FT TURN 52..55
FT /evidence="ECO:0007829|PDB:3FOZ"
FT HELIX 59..64
FT /evidence="ECO:0007829|PDB:3FOZ"
FT STRAND 67..71
FT /evidence="ECO:0007829|PDB:2ZM5"
FT HELIX 81..97
FT /evidence="ECO:0007829|PDB:3FOZ"
FT STRAND 101..107
FT /evidence="ECO:0007829|PDB:3FOZ"
FT HELIX 109..116
FT /evidence="ECO:0007829|PDB:3FOZ"
FT HELIX 127..152
FT /evidence="ECO:0007829|PDB:3FOZ"
FT HELIX 154..159
FT /evidence="ECO:0007829|PDB:3FOZ"
FT HELIX 165..178
FT /evidence="ECO:0007829|PDB:3FOZ"
FT HELIX 182..186
FT /evidence="ECO:0007829|PDB:3FOZ"
FT STRAND 194..203
FT /evidence="ECO:0007829|PDB:3FOZ"
FT HELIX 207..223
FT /evidence="ECO:0007829|PDB:3FOZ"
FT HELIX 226..236
FT /evidence="ECO:0007829|PDB:3FOZ"
FT TURN 244..247
FT /evidence="ECO:0007829|PDB:3FOZ"
FT HELIX 251..259
FT /evidence="ECO:0007829|PDB:3FOZ"
FT HELIX 264..287
FT /evidence="ECO:0007829|PDB:3FOZ"
FT STRAND 293..296
FT /evidence="ECO:0007829|PDB:3FOZ"
FT HELIX 300..308
FT /evidence="ECO:0007829|PDB:3FOZ"
SQ SEQUENCE 316 AA; 35065 MW; FBFDC18770781C8F CRC64;
MSDISKASLP KAIFLMGPTA SGKTALAIEL RKILPVELIS VDSALIYKGM DIGTAKPNAE
ELLAAPHRLL DIRDPSQAYS AADFRRDALA EMADITAAGR IPLLVGGTML YFKALLEGLS
PLPSADPEVR ARIEQQAAEQ GWESLHRQLQ EVDPVAAARI HPNDPQRLSR ALEVFFISGK
TLTELTQTSG DALPYQVHQF AIAPASRELL HQRIEQRFHQ MLASGFEAEV RALFARGDLH
TDLPSIRCVG YRQMWSYLEG EISYDEMVYR GVCATRQLAK RQITWLRGWE GVHWLDSEKP
EQARDEVLQV VGAIAG
