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Escherichia coli K-12 substr. MG1655 Enzyme: tRNA(i6A37) synthase



Gene: miaA Accession Numbers: EG10595 (EcoCyc), b4171, ECK4167

Synonyms: trpX

Regulation Summary Diagram: ?

Summary:
Dimethylallyl diphosphate:tRNA dimethylallyltransferase (DMAPP-tRNA transferase, MiaA) catalyzes the first step in the pathway for hypermodification of the A37 base of certain tRNAs such as tRNATyr and tRNAPhe. The enzyme transfers the dimethylallyl moiety of DMAPP to the N6 position of A37, which is adjacent to the anticodon [Rosenbaum72, Bartz70]. This modification is important in preventing frameshifts and other mutations [Urbonavicius01]. Further thiomethylation of the A37 position is dependent on the presence of the isopentenyl modification [Vold79].

MiaA can act on isolated tRNA stem-loops, as long as the helix stem and the A36-A37-A38 motif are both present [Motorin97, Soderberg00]. Co-crystal structures of MiaA in complex with tRNAPhe have been solved, showing a mutually induced fit mechanism of recognition involving structural rearrangement of the anticodon loop of the tRNA [Seif09, Chimnaronk09]. No substantial change in the structure of the catalytic domain of MiaA is seen upon tRNA binding [Chimnaronk09]. Both reports rely for comparison on apo-MiaA structures of the protein from other organisms. An ordered sequential mechanism of substrate binding and catalysis has been suggested [Moore97a, Moore00a].

Modification of tRNAs by MiaA is important in preventing various mutations. miaA mutants show increased +1 (but not -1) frameshifting as well as GC to TA transversions, the latter requiring active recombination [Urbonavicius01, Urbonavicius03, Connolly91a, Zhao01a]. miaA mutations also increase the general rate of spontaneous mutations and alter readthrough and suppression of nonsense codons [Connolly89, Petrullo83].

In miaA mutants, the altered efficiency of translation by tRNAs lacking the dimethylallyl modification affects regulation by attenuation of several operons, including pheA, trp, pheMST and tnaCA [Gowrishankar82, Springer83, Vacher84, Gollnick90a, Pages90, Landick90a]. A mutation in miaA inhibits growth and, when combined with a mutation in rpsL, leads to streptomycin dependence [Diaz87, Diaz86]. A miaA mutation is lethal in a strain lacking functional tRNA6Leu [Nakayashiki98]. Deletion of miaA increases the evolvability of resistance to ciprofloxacin [Mehi13]. A miaA insertion mutant shows decreased levels of RpoS, consistent with a MiaA requirement for efficient RpoS translation [Thompson14].

The miaA gene is part of a superoperon with complex patterns of transcription and mechanisms of regulation [Tsui94a]. The superoperon includes a number of heat shock promoters, and miaA is essential for growth at high temperatures [Tsui96].

Review: [El12]

Gene Citations: [Nonaka06, Kitagawa96, Tsui94]

Locations: cytosol

Map Position: [4,397,275 -> 4,398,225] (94.78 centisomes)
Length: 951 bp / 316 aa

Molecular Weight of Polypeptide: 35.065 kD (from nucleotide sequence), 33.5 kD (experimental) [Connolly89 ]

Unification Links: ASAP:ABE-0013657 , CGSC:18160 , EchoBASE:EB0590 , EcoGene:EG10595 , EcoliWiki:b4171 , OU-Microarray:b4171 , PortEco:miaA , PR:PRO_000023235 , Pride:P16384 , Protein Model Portal:P16384 , RefSeq:NP_418592 , RegulonDB:EG10595 , SMR:P16384 , String:511145.b4171 , UniProt:P16384

Relationship Links: InterPro:IN-FAMILY:IPR002627 , InterPro:IN-FAMILY:IPR018022 , InterPro:IN-FAMILY:IPR027417 , Panther:IN-FAMILY:PTHR11088 , PDB:PART-OF:2ZM5 , PDB:PART-OF:2ZXU , PDB:PART-OF:3FOZ , Pfam:IN-FAMILY:PF01715

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006400 - tRNA modification Inferred from experiment [Vold79, Eisenberg79b]
GO:0034605 - cellular response to heat Inferred from experiment [Tsui96]
GO:0008033 - tRNA processing Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
Molecular Function: GO:0052381 - tRNA dimethylallyltransferase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, Rosenbaum72]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005737 - cytoplasm
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: cell processes adaptations temperature extremes
information transfer RNA related RNA modification

Essentiality data for miaA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]

Credits:
Last-Curated ? 20-Dec-2013 by Keseler I , SRI International


Enzymatic reaction of: tRNA(i6A37) synthase

Synonyms: tRNA isopentenyltransferase, isopentenyl-diphosphate:tRNA isopentenyltransferase, IPP transferase, transfer ribonucleate isopentenyltransferase, D2-isopentenyl pyrophosphate:tRNA-D2-isopentenyl transferase, D2-isopentenyl pyrophosphate:transfer ribonucleic acid D2-isopentenyltransferase, Δ2-isopentenylpyrophosphate tRNA-adenosine transferase, dimethylallyl diphosphate:tRNA dimethylallyltransferase

EC Number: 2.5.1.75

dimethylallyl diphosphate + an adenosine37 in tRNA <=> N6-dimethylallyladenosine37 in tRNA + diphosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

Reversibility of this reaction is unspecified.

Summary:
In addition to the Km values reported below, a different study found a Km for tRNA substrates of 3 nM and for dimethylallyl diphosphate of 632 nM [Leung97].

Cofactors or Prosthetic Groups: Mg2+ [Moore97a, Rosenbaum72]

Inhibitors (Competitive): ATP [Leung97] , ADP [Leung97]

Inhibitors (Unknown Mechanism): diphosphate [Rosenbaum72]

Kinetic Parameters:

Substrate
Km (μM)
Citations
dimethylallyl diphosphate
0.63
[Leung97, BRENDA14]
dimethylallyl diphosphate
2200.0
[Soderberg01a, BRENDA14]
dimethylallyl diphosphate
3.2, 3.2
[Moore97a, BRENDA14]

pH(opt): 6.5 [BRENDA14, Moore97a], 7.5 [Rosenbaum72]


Sequence Features

Feature Class Location Citations Comment
Nucleotide-Phosphate-Binding-Region 17 -> 24
[UniProt10]
UniProt: ATP; Non-Experimental Qualifier: potential;
Protein-Segment 19 -> 24
[UniProt10]
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity;
Protein-Segment 42 -> 45
[UniProt10]
UniProt: Interaction with substrate tRNA; Sequence Annotation Type: region of interest;
Sequence-Conflict 101
[Noble93, UniProt10a]
Alternate sequence: I → D; UniProt: (in Ref. 7; AAC43396);
Amino-Acid-Site 108
[UniProt10a]
UniProt: Interaction with substrate tRNA; Sequence Annotation Type: site;
Protein-Segment 120 -> 124
[UniProt10]
UniProt: Interaction with substrate tRNA; Sequence Annotation Type: region of interest;
Amino-Acid-Site 130
[UniProt10a]
UniProt: Interaction with substrate tRNA; Sequence Annotation Type: site;
Protein-Segment 166 -> 170
[UniProt10]
UniProt: Interaction with substrate tRNA; Sequence Annotation Type: region of interest;
Protein-Segment 206 -> 229
[UniProt10]
UniProt: Interaction with isopentenylpyrophosphate transferase; Sequence Annotation Type: region of interest;
Protein-Segment 247 -> 252
[UniProt10]
UniProt: Interaction with substrate tRNA; Sequence Annotation Type: region of interest;
Amino-Acid-Site 280
[UniProt10a]
UniProt: Required for specificity towards tRNA substrates containing a purine at position 29; Sequence Annotation Type: site;
Protein-Segment 280 -> 287
[UniProt10]
UniProt: Interaction with substrate tRNA; Sequence Annotation Type: region of interest;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b4171 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10595; confirmed by SwissProt match.


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Bartz70: Bartz JK, Kline LK, Soll D (1970). "N6-(Delta 2-isopentenyl)adenosine: biosynthesis in vitro in transfer RNA by an enzyme purified from Escherichia coli." Biochem Biophys Res Commun 40(6);1481-7. PMID: 4326583

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Caillet88: Caillet J, Droogmans L (1988). "Molecular cloning of the Escherichia coli miaA gene involved in the formation of delta 2-isopentenyl adenosine in tRNA." J Bacteriol 170(9);4147-52. PMID: 3045085

Chimnaronk09: Chimnaronk S, Forouhar F, Sakai J, Yao M, Tron CM, Atta M, Fontecave M, Hunt JF, Tanaka I (2009). "Snapshots of dynamics in synthesizing N(6)-isopentenyladenosine at the tRNA anticodon." Biochemistry 48(23);5057-65. PMID: 19435325

Connolly89: Connolly DM, Winkler ME (1989). "Genetic and physiological relationships among the miaA gene, 2-methylthio-N6-(delta 2-isopentenyl)-adenosine tRNA modification, and spontaneous mutagenesis in Escherichia coli K-12." J Bacteriol 171(6);3233-46. PMID: 2656644

Connolly91a: Connolly DM, Winkler ME (1991). "Structure of Escherichia coli K-12 miaA and characterization of the mutator phenotype caused by miaA insertion mutations." J Bacteriol 173(5);1711-21. PMID: 1999389

Diaz86: Diaz I, Ehrenberg M, Kurland CG (1986). "How do combinations of rpsL- and miaA- generate streptomycin dependence?." Mol Gen Genet 202(2);207-11. PMID: 3517592

Diaz87: Diaz I, Pedersen S, Kurland CG (1987). "Effects of miaA on translation and growth rates." Mol Gen Genet 208(3);373-6. PMID: 3312947

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Eisenberg79b: Eisenberg SP, Yarus M, Soll L (1979). "The effect of an Escherichia coli regulatory mutation on transfer RNA structure." J Mol Biol 135(1);111-26. PMID: 93644

El12: El Yacoubi B, Bailly M, de Crecy-Lagard V (2012). "Biosynthesis and function of posttranscriptional modifications of transfer RNAs." Annu Rev Genet 46;69-95. PMID: 22905870

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Gollnick90a: Gollnick P, Yanofsky C (1990). "tRNA(Trp) translation of leader peptide codon 12 and other factors that regulate expression of the tryptophanase operon." J Bacteriol 1990;172(6);3100-7. PMID: 2345136

Gowrishankar82: Gowrishankar J, Pittard J (1982). "Regulation of phenylalanine biosynthesis in Escherichia coli K-12: control of transcription of the pheA operon." J Bacteriol 150(3);1130-7. PMID: 7042684

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kitagawa96: Kitagawa R, Mitsuki H, Okazaki T, Ogawa T (1996). "A novel DnaA protein-binding site at 94.7 min on the Escherichia coli chromosome." Mol Microbiol 1996;19(5);1137-47. PMID: 8830270

Landick90a: Landick R, Yanofsky C, Choo K, Phung L (1990). "Replacement of the Escherichia coli trp operon attenuation control codons alters operon expression." J Mol Biol 216(1);25-37. PMID: 2231731

Leung97: Leung HC, Chen Y, Winkler ME (1997). "Regulation of substrate recognition by the MiaA tRNA prenyltransferase modification enzyme of Escherichia coli K-12." J Biol Chem 272(20);13073-83. PMID: 9148919

Mehi13: Mehi O, Bogos B, Csorgo B, Pal C (2013). "Genomewide screen for modulators of evolvability under toxic antibiotic exposure." Antimicrob Agents Chemother 57(7);3453-6. PMID: 23669383

Moore00a: Moore JA, Mathis JR, Poulter CD (2000). "Escherichia coli dimethylallyl diphosphate:tRNA dimethylallyltransferase: pre-steady-state kinetic studies." Biochim Biophys Acta 1479(1-2);166-74. PMID: 11004538

Moore97a: Moore JA, Poulter CD (1997). "Escherichia coli dimethylallyl diphosphate:tRNA dimethylallyltransferase: a binding mechanism for recombinant enzyme." Biochemistry 36(3);604-14. PMID: 9012675

Motorin97: Motorin Y, Bec G, Tewari R, Grosjean H (1997). "Transfer RNA recognition by the Escherichia coli delta2-isopentenyl-pyrophosphate:tRNA delta2-isopentenyl transferase: dependence on the anticodon arm structure." RNA 3(7);721-33. PMID: 9214656

Nakayashiki98: Nakayashiki T, Inokuchi H (1998). "Novel temperature-sensitive mutants of Escherichia coli that are unable to grow in the absence of wild-type tRNA6Leu." J Bacteriol 180(11);2931-5. PMID: 9603884

Noble93: Noble J.A., Innis M.A., Banuett F., Herskowitz I. (1993). Data submission to EMBL/GenBank/DDBJ databases on 1993-05.

Nonaka06: Nonaka G, Blankschien M, Herman C, Gross CA, Rhodius VA (2006). "Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress." Genes Dev 20(13);1776-89. PMID: 16818608

Pages90: Pages D, Buckingham RH (1990). "Mutants of pheV in Escherichia coli affecting control by attenuation of the pheS, T and pheA operons. Two distinct mechanisms for de-attenuation." J Mol Biol 216(1);17-24. PMID: 2231729

Petrullo83: Petrullo LA, Gallagher PJ, Elseviers D (1983). "The role of 2-methylthio-N6-isopentenyladenosine in readthrough and suppression of nonsense codons in Escherichia coli." Mol Gen Genet 190(2);289-94. PMID: 6410151

Rosenbaum72: Rosenbaum N, Gefter ML (1972). "Delta 2 -isopentenylpyrophosphate: transfer ribonucleic acid 2 -isopentenyltransferase from Escherichia coli. Purification and properties of the enzyme." J Biol Chem 247(18);5675-80. PMID: 4341485

Seif09: Seif E, Hallberg BM (2009). "RNA-protein mutually induced fit: structure of Escherichia coli isopentenyl-tRNA transferase in complex with tRNA(Phe)." J Biol Chem 284(11);6600-4. PMID: 19158097

Soderberg00: Soderberg T, Poulter CD (2000). "Escherichia coli dimethylallyl diphosphate:tRNA dimethylallyltransferase: essential elements for recognition of tRNA substrates within the anticodon stem-loop." Biochemistry 39(21);6546-53. PMID: 10828971

Soderberg01a: Soderberg T, Poulter CD (2001). "Escherichia coli dimethylallyl diphosphate:tRNA dimethylallyltransferase: site-directed mutagenesis of highly conserved residues." Biochemistry 40(6);1734-40. PMID: 11327834

Springer83: Springer M, Trudel M, Graffe M, Plumbridge J, Fayat G, Mayaux JF, Sacerdot C, Blanquet S, Grunberg-Manago M (1983). "Escherichia coli phenylalanyl-tRNA synthetase operon is controlled by attenuation in vivo." J Mol Biol 171(3);263-79. PMID: 6317866

Thompson14: Thompson KM, Gottesman S (2014). "The MiaA tRNA modification enzyme is necessary for robust RpoS expression in Escherichia coli." J Bacteriol 196(4);754-61. PMID: 24296670

Tsui94: Tsui HC, Leung HC, Winkler ME (1994). "Characterization of broadly pleiotropic phenotypes caused by an hfq insertion mutation in Escherichia coli K-12." Mol Microbiol 13(1);35-49. PMID: 7984093

Tsui94a: Tsui HC, Winkler ME (1994). "Transcriptional patterns of the mutL-miaA superoperon of Escherichia coli K-12 suggest a model for posttranscriptional regulation." Biochimie 76(12);1168-77. PMID: 7748952

Tsui96: Tsui HC, Feng G, Winkler ME (1996). "Transcription of the mutL repair, miaA tRNA modification, hfq pleiotropic regulator, and hflA region protease genes of Escherichia coli K-12 from clustered Esigma32-specific promoters during heat shock." J Bacteriol 178(19);5719-31. PMID: 8824618

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Urbonavicius01: Urbonavicius J, Qian Q, Durand JM, Hagervall TG, Bjork GR (2001). "Improvement of reading frame maintenance is a common function for several tRNA modifications." EMBO J 20(17);4863-73. PMID: 11532950

Urbonavicius03: Urbonavicius J, Stahl G, Durand JM, Ben Salem SN, Qian Q, Farabaugh PJ, Bjork GR (2003). "Transfer RNA modifications that alter +1 frameshifting in general fail to affect -1 frameshifting." RNA 9(6);760-8. PMID: 12756333

Vacher84: Vacher J, Grosjean H, Houssier C, Buckingham RH (1984). "The effect of point mutations affecting Escherichia coli tryptophan tRNA on anticodon-anticodon interactions and on UGA suppression." J Mol Biol 177(2);329-42. PMID: 6379198

Vold79: Vold BS, Lazar JM, Gray AM (1979). "Characterization of a deficiency of N6-(delta 2-isopentenyl)-2-methylthioadenosine in the Escherichia coli mutant trpX by use of antibodies to N6-(delta 2-isopentenyl)adenosine." J Biol Chem 254(15);7362-7. PMID: 379002

Zhao01a: Zhao J, Leung HE, Winkler ME (2001). "The miaA mutator phenotype of Escherichia coli K-12 requires recombination functions." J Bacteriol 183(5);1796-800. PMID: 11160115

Other References Related to Gene Regulation

Maciag11a: Maciag A, Peano C, Pietrelli A, Egli T, De Bellis G, Landini P (2011). "In vitro transcription profiling of the {sigma}S subunit of bacterial RNA polymerase: re-definition of the {sigma}S regulon and identification of {sigma}S-specific promoter sequence elements." Nucleic Acids Res 39(13);5338-55. PMID: 21398637

Mangat08: Mangat CS, Brown ED (2008). "Known bioactive small molecules probe the function of a widely conserved but enigmatic bacterial ATPase, YjeE." Chem Biol 15(12);1287-95. PMID: 19101473


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Fri Nov 28, 2014, biocyc13.