Escherichia coli K-12 substr. MG1655 Enzyme: tRNA m1G37 methyltransferase

Gene: trmD Accession Numbers: EG11023 (EcoCyc), b2607, ECK2604

Regulation Summary Diagram: ?

Regulation summary diagram for trmD

Subunit composition of tRNA m1G37 methyltransferase = [TrmD]2
         tRNA m1G37 methyltransferase = TrmD

tRNA m1G37 methyltransferase (TrmD) catalyzes the addition of a methyl group to G37 of certain tRNAs [Hjalmarsson83, Bjork78, Bystrom82]. Specificity of this activity is controlled by tRNA structure, specifically including the V, T and D side loops and the presence of G36pG37 [Holmes92, Redlak97]. TrmD can accomodate both A and G at position 36 in tRNAAsp and tRNAPhe [Brule04]. Analysis of enzyme activity with truncated tRNAs showed that TrmD minimally requires the anticodon loop and a 9 bp stem in vitro, distinguishing the prokaryotic enzymes from the archaeal and eukaryotic Trm5 [Christian07].

The crystal structure of the TrmD homodimer bound to S-adenosyl homocysteine was determined to 2.5 Å resolution. Predicted active site residues were mutagenized, and the kinetic parameters of the resulting enzymes were analyzed [Elkins03a]. Protection of tRNA and conformational changes during methylation have been analyzed [Gabryszuk97, Watts05]. Pre-steady state kinetic analysis showed that, unlike the archaeal Trm5 enzyme, TrmD does not show burst kinetics, and only one of the two active sites in the dimeric enzyme is functional at any given time [Christian10]. Adenosine and methionine competitively inhibit TrmD, but not Trm5 [Lahoud11].

The originally isolated trmD mutant is a temperature-sensitive allele [Bjork78a, Bjork78]. Non-polar trmD mutants grow several fold slower [Persson95] and experience more frameshifting than wild-type E. coli [Urbonavicius01]. A high-throughput experiment identified the trmD gene as essential for growth [Baba06]. trmD has been the subject of a pilot study to screen for genetic interactions with null alleles in the Keio collection [Yong13].

The level of TrmD activity is not growth rate-dependent [Ny80]. The enzyme is present in very low amounts [Hjalmarsson83]. TrmD is encoded within an operon together with the ribosomal proteins S16 and L19, and its lower abundance appears to be regulated at the translational level [Wikstrom88].

TrmD: "tRNA methylation" [Bjork78]

Review: [Holmes95]

Citations: [Wang13b]

Gene Citations: [Bystrom89]

Locations: cytosol

Map Position: [2,742,594 <- 2,743,361] (59.11 centisomes, 213°)
Length: 768 bp / 255 aa

Molecular Weight of Polypeptide: 28.422 kD (from nucleotide sequence), 32.0 kD (experimental) [Hjalmarsson83 ]

Molecular Weight of Multimer: 46.0 kD (experimental) [Hjalmarsson83]

pI: 5.2 [Hjalmarsson83]

Unification Links: ASAP:ABE-0008576 , CGSC:76 , DIP:DIP-48264N , EchoBASE:EB1016 , EcoGene:EG11023 , EcoliWiki:b2607 , ModBase:P0A873 , OU-Microarray:b2607 , PortEco:trmD , Pride:P0A873 , Protein Model Portal:P0A873 , RefSeq:NP_417098 , RegulonDB:EG11023 , SMR:P0A873 , String:511145.b2607 , UniProt:P0A873

Relationship Links: InterPro:IN-FAMILY:IPR002649 , InterPro:IN-FAMILY:IPR016009 , InterPro:IN-FAMILY:IPR023148 , InterPro:IN-FAMILY:IPR029026 , InterPro:IN-FAMILY:IPR029028 , PDB:Structure:1P9P , Pfam:IN-FAMILY:PF01746

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for trmD

GO Terms:

Biological Process: GO:0002939 - tRNA N1-guanine methylation Inferred from experiment [Hjalmarsson83]
GO:0030488 - tRNA methylation Inferred from experiment [Bjork78]
GO:0006400 - tRNA modification Inferred by computational analysis [GOA06]
GO:0008033 - tRNA processing Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0032259 - methylation Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0009019 - tRNA (guanine-N1-)-methyltransferase activity Inferred from experiment Inferred by computational analysis [GOA06, Elkins03a, Hjalmarsson83]
GO:0042802 - identical protein binding Inferred from experiment [Rajagopala14, Rajagopala12]
GO:0042803 - protein homodimerization activity Inferred from experiment [Hjalmarsson83]
GO:0052906 - tRNA (guanine(37)-N(1))-methyltransferase activity Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, Elkins03a]
GO:0008168 - methyltransferase activity Inferred by computational analysis [UniProtGOA11]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0050518 - 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity Inferred by computational analysis [Gaudet10]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06]

MultiFun Terms: information transfer RNA related RNA modification

Essentiality data for trmD knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 1]

Created 15-Mar-2006 by Shearer A , SRI International
Curated 15-Mar-2006 by Shearer A , SRI International
Last-Curated ? 05-Apr-2013 by Keseler I , SRI International

Enzymatic reaction of: tRNA m1G37 methyltransferase

Synonyms: tRNA (guanine-N1-)-methyltransferase

EC Number:

guanine37 in tRNA + S-adenosyl-L-methionine <=> N1-methylguanine37 in tRNA + S-adenosyl-L-homocysteine + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Cofactors or Prosthetic Groups: Mg2+ [Brule04]

Inhibitors (Competitive): sinefungin (Kic = 0.62µM) [Lahoud11] , adenosine (Kic = 34.7µM) [Lahoud11] , S-adenosyl-L-homocysteine (Kic = 6µM) [Hjalmarsson83, Lahoud11]

Kinetic Parameters:

Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
guanine37 in tRNA
guanine37 in tRNA

T(opt): 37 °C [BRENDA14, Christian07]

pH(opt): 7.4 [Brule04]

Sequence Features

Protein sequence of tRNA m1G37 methyltransferase with features indicated

Feature Class Location Citations Comment
Mutagenesis-Variant 59
[Elkins03a, UniProt11]
UniProt: Loss of activity.
Amino-Acid-Sites-That-Bind 86
UniProt: S-adenosyl-L-methionine.
Mutagenesis-Variant 91
[Elkins03a, UniProt11]
UniProt: Loss of activity; no effect on tRNA binding.
Amino-Acid-Sites-That-Bind 113
UniProt: S-adenosyl-L-methionine; via amide nitrogen; Non-Experimental Qualifier: by similarity;
Mutagenesis-Variant 114
[Elkins03a, UniProt11]
UniProt: Loss of activity.
Mutagenesis-Variant 115
[Elkins03a, UniProt11]
UniProt: Increases Km for S-adenosyl-L- methionine 24-fold.
Mutagenesis-Variant 117
[Elkins03a, UniProt11]
UniProt: Loss of activity.
Mutagenesis-Variant 119
[Elkins03a, UniProt11]
UniProt: Loss of activity.
Mutagenesis-Variant 121
[Elkins03a, UniProt11]
UniProt: Loss of activity; no effect on tRNA binding.
Mutagenesis-Variant 128
[Elkins03a, UniProt11]
UniProt: Loss of activity.
Protein-Segment 133 -> 138
UniProt: S-adenosyl-L-methionine binding; Sequence Annotation Type: region of interest;
Mutagenesis-Variant 135
[Elkins03a, UniProt11]
UniProt: Loss of activity; no effect on tRNA binding.
Mutagenesis-Variant 136
[Elkins03a, UniProt11]
UniProt: Increases Km for S-adenosyl-L- methionine 68-fold.
Mutagenesis-Variant 141
[Elkins03a, UniProt11]
UniProt: Increases Km for S-adenosyl-L- methionine 82-fold.
Mutagenesis-Variant 154
[Elkins03a, UniProt11]
UniProt: Loss of activity; no effect on tRNA binding.
Mutagenesis-Variant 169
[Elkins03a, UniProt11]
UniProt: Loss of activity.
Active-Site 169
UniProt: Proton acceptor; Non-Experimental Qualifier: potential;
Mutagenesis-Variant 171
[Elkins03a, UniProt11]
UniProt: Loss of activity.
Mutagenesis-Variant 184
[Elkins03a, UniProt11]
UniProt: Loss of activity; no effect on tRNA binding.
Mutagenesis-Variant 192
[Elkins03a, UniProt11]
UniProt: Loss of activity; no effect on tRNA binding.
Mutagenesis-Variant 193
[Elkins03a, UniProt11]
UniProt: Loss of activity; no effect on tRNA binding.
Mutagenesis-Variant 196
[Elkins03a, UniProt11]
UniProt: Loss of activity; no effect on tRNA binding.
Mutagenesis-Variant 197
[Elkins03a, UniProt11]
UniProt: Loss of activity; no effect on tRNA binding.
Mutagenesis-Variant 204
[Elkins03a, UniProt11]
UniProt: Loss of activity; no effect on tRNA binding.
Mutagenesis-Variant 207
[Elkins03a, UniProt11]
[Elkins03a, UniProt11]
W → A: Loss of activity; no effect on tRNA binding.
W → F or H: Small decrease in activity.
Mutagenesis-Variant 208
[Elkins03a, UniProt11]
UniProt: Loss of activity; no effect on tRNA binding.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b2607 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11023; confirmed by SwissProt match.


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

Bjork78: Bjork GR, Kjellin-Straby K (1978). "Escherichia coli mutants with defects in the biosynthesis of 5-methylaminomethyl-2-thio-uridine or 1-methylguanosine in their tRNA." J Bacteriol 133(2);508-17. PMID: 342495

Bjork78a: Bjork GR, Kjellin-Straby K (1978). "General screening procedure for RNA modificationless mutants: isolation of Escherichia coli strains with specific defects in RNA methylation." J Bacteriol 133(2);499-507. PMID: 342494

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014."

Brule04: Brule H, Elliott M, Redlak M, Zehner ZE, Holmes WM (2004). "Isolation and characterization of the human tRNA-(N1G37) methyltransferase (TRM5) and comparison to the Escherichia coli TrmD protein." Biochemistry 43(28);9243-55. PMID: 15248782

Bystrom82: Bystrom AS, Bjork GR (1982). "Chromosomal location and cloning of the gene (trmD) responsible for the synthesis of tRNA (m1G) methyltransferase in Escherichia coli K-12." Mol Gen Genet 188(3);440-6. PMID: 6298573

Bystrom89: Bystrom AS, von Gabain A, Bjork GR (1989). "Differentially expressed trmD ribosomal protein operon of Escherichia coli is transcribed as a single polycistronic mRNA species." J Mol Biol 208(4);575-86. PMID: 2478711

Christian07: Christian T, Hou YM (2007). "Distinct determinants of tRNA recognition by the TrmD and Trm5 methyl transferases." J Mol Biol 373(3);623-32. PMID: 17868690

Christian10: Christian T, Lahoud G, Liu C, Hou YM (2010). "Control of catalytic cycle by a pair of analogous tRNA modification enzymes." J Mol Biol 400(2);204-17. PMID: 20452364

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

Elkins03a: Elkins PA, Watts JM, Zalacain M, van Thiel A, Vitazka PR, Redlak M, Andraos-Selim C, Rastinejad F, Holmes WM (2003). "Insights into catalysis by a knotted TrmD tRNA methyltransferase." J Mol Biol 333(5);931-49. PMID: 14583191

Gabryszuk97: Gabryszuk J, Holmes WM (1997). "tRNA recognition for modification: solution probing of tRNA complexed with Escherichia coli tRNA (guanosine-1) methyltransferase." RNA 3(11);1327-36. PMID: 9409623

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

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."

Hjalmarsson83: Hjalmarsson KJ, Bystrom AS, Bjork GR (1983). "Purification and characterization of transfer RNA (guanine-1)methyltransferase from Escherichia coli." J Biol Chem 258(2);1343-51. PMID: 6337136

Holmes92: Holmes WM, Andraos-Selim C, Roberts I, Wahab SZ (1992). "Structural requirements for tRNA methylation. Action of Escherichia coli tRNA(guanosine-1)methyltransferase on tRNA(1Leu) structural variants." J Biol Chem 267(19);13440-5. PMID: 1618846

Holmes95: Holmes WM, Andraos-Selim C, Redlak M (1995). "tRNA-m1G methyltransferase interactions: touching bases with structure." Biochimie 77(1-2);62-5. PMID: 7599277

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Lahoud11: Lahoud G, Goto-Ito S, Yoshida K, Ito T, Yokoyama S, Hou YM (2011). "Differentiating analogous tRNA methyltransferases by fragments of the methyl donor." RNA 17(7);1236-46. PMID: 21602303

Ny80: Ny T, Thomale J, Hjalmarsson K, Nass G, Bjork GR (1980). "Non-coordinate regulation of enzymes involved in transfer RNA metabolism in Escherichia coli." Biochim Biophys Acta 607(2);277-84. PMID: 6154481

Persson95: Persson BC, Bylund GO, Berg DE, Wikstrom PM (1995). "Functional analysis of the ffh-trmD region of the Escherichia coli chromosome by using reverse genetics." J Bacteriol 177(19);5554-60. PMID: 7559342

Rajagopala12: Rajagopala SV, Sikorski P, Caufield JH, Tovchigrechko A, Uetz P (2012). "Studying protein complexes by the yeast two-hybrid system." Methods 58(4);392-9. PMID: 22841565

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Redlak97: Redlak M, Andraos-Selim C, Giege R, Florentz C, Holmes WM (1997). "Interaction of tRNA with tRNA (guanosine-1)methyltransferase: binding specificity determinants involve the dinucleotide G36pG37 and tertiary structure." Biochemistry 36(29);8699-709. PMID: 9220956

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

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

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms 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

Wang13b: Wang P, Yang L, Liu P, Gao YQ, Zhao XS (2013). "Single-molecule detection reveals knot sliding in TrmD denaturation." Chemistry 19(19);5909-16. PMID: 23512842

Watts05: Watts JM, Gabruzsk J, Holmes WM (2005). "Ligand-mediated anticodon conformational changes occur during tRNA methylation by a TrmD methyltransferase." Biochemistry 44(17);6629-39. PMID: 15850396

Wikstrom88: Wikstrom PM, Bjork GR (1988). "Noncoordinate translation-level regulation of ribosomal and nonribosomal protein genes in the Escherichia coli trmD operon." J Bacteriol 170(7);3025-31. PMID: 3290194

Yong13: Yong HT, Yamamoto N, Takeuchi R, Hsieh YJ, Conrad TM, Datsenko KA, Nakayashiki T, Wanner BL, Mori H (2013). "Development of a system for discovery of genetic interactions for essential genes in Escherichia coli K-12." Genes Genet Syst 88(4);233-40. PMID: 24463526

Other References Related to Gene Regulation

Lemke11: Lemke JJ, Sanchez-Vazquez P, Burgos HL, Hedberg G, Ross W, Gourse RL (2011). "Direct regulation of Escherichia coli ribosomal protein promoters by the transcription factors ppGpp and DksA." Proc Natl Acad Sci U S A 108(14);5712-7. PMID: 21402902

Salmon03: Salmon K, Hung SP, Mekjian K, Baldi P, Hatfield GW, Gunsalus RP (2003). "Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR." J Biol Chem 278(32);29837-55. PMID: 12754220

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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