TRMD_ECOLI
ID TRMD_ECOLI Reviewed; 255 AA.
AC P0A873; P07020;
DT 01-APR-1988, integrated into UniProtKB/Swiss-Prot.
DT 01-APR-1988, sequence version 1.
DT 03-AUG-2022, entry version 128.
DE RecName: Full=tRNA (guanine-N(1)-)-methyltransferase;
DE EC=2.1.1.228 {ECO:0000269|PubMed:14583191};
DE AltName: Full=M1G-methyltransferase;
DE AltName: Full=tRNA [GM37] methyltransferase;
GN Name=trmD; OrderedLocusNames=b2607, JW2588;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND OPERON STRUCTURE.
RC STRAIN=K12;
RX PubMed=6357787; DOI=10.1002/j.1460-2075.1983.tb01519.x;
RA Bystroem A.S., Hjalmarsson K.J., Wikstroem P.M., Bjoerk G.R.;
RT "The nucleotide sequence of an Escherichia coli operon containing genes for
RT the tRNA(m1G)methyltransferase, the ribosomal proteins S16 and L19 and a
RT 21-K polypeptide.";
RL EMBO J. 2:899-905(1983).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9205837; DOI=10.1093/dnares/4.2.91;
RA Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K.,
RA Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T., Oyama S.,
RA Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H.,
RA Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.;
RT "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12
RT genome corresponding to 50.0-68.8 min on the linkage map and analysis of
RT its sequence features.";
RL DNA Res. 4:91-113(1997).
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 CHARACTERIZATION, AND PROTEIN SEQUENCE OF 1-10.
RX PubMed=6337136; DOI=10.1016/s0021-9258(18)33199-5;
RA Hjalmarsson K.J., Bystroem A.S., Bjoerk G.R.;
RT "Purification and characterization of transfer RNA (guanine-
RT 1)methyltransferase from Escherichia coli.";
RL J. Biol. Chem. 258:1343-1351(1983).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH SUBSTRATE, FUNCTION,
RP SUBUNIT, MUTAGENESIS OF GLY-59; GLY-91; ARG-114; TYR-115; GLY-117; ASP-119;
RP ARG-121; ASP-128; ASP-135; TYR-136; GLY-141; ARG-154; ASP-169; PHE-171;
RP PRO-184; VAL-192; PRO-193; LEU-196; LEU-197; ILE-204; TRP-207 AND ARG-208,
RP ACTIVE SITE, AND CATALYTIC ACTIVITY.
RX PubMed=14583191; DOI=10.1016/j.jmb.2003.09.011;
RA Elkins P.A., Watts J.M., Zalacain M., van Thiel A., Vitazka P.R.,
RA Redlak M., Andraos-Selim C., Rastinejad F., Holmes W.M.;
RT "Insights into catalysis by a knotted TrmD tRNA methyltransferase.";
RL J. Mol. Biol. 333:931-949(2003).
CC -!- FUNCTION: Specifically methylates guanosine-37 in various tRNAs.
CC {ECO:0000269|PubMed:14583191}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=guanosine(37) in tRNA + S-adenosyl-L-methionine = H(+) + N(1)-
CC methylguanosine(37) in tRNA + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:36899, Rhea:RHEA-COMP:10145, Rhea:RHEA-COMP:10147,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:73542, ChEBI:CHEBI:74269; EC=2.1.1.228;
CC Evidence={ECO:0000269|PubMed:14583191};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:14583191}.
CC -!- INTERACTION:
CC P0A873; P0A873: trmD; NbExp=3; IntAct=EBI-1129132, EBI-1129132;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- INDUCTION: Part of the rpsP-rimM-trmD-rplS operon.
CC -!- MISCELLANEOUS: The specific activity of this enzyme increases only
CC slightly with increased growth rate.
CC -!- MISCELLANEOUS: This enzyme is present at ca. 80 molecules/genome.
CC -!- SIMILARITY: Belongs to the RNA methyltransferase TrmD family.
CC {ECO:0000305}.
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DR EMBL; X01818; CAA25959.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75656.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA16492.1; -; Genomic_DNA.
DR PIR; A30380; XYECG1.
DR RefSeq; NP_417098.1; NC_000913.3.
DR RefSeq; WP_000264777.1; NZ_STEB01000040.1.
DR PDB; 1P9P; X-ray; 2.50 A; A=1-255.
DR PDBsum; 1P9P; -.
DR AlphaFoldDB; P0A873; -.
DR SMR; P0A873; -.
DR BioGRID; 4263072; 57.
DR BioGRID; 851435; 1.
DR DIP; DIP-48264N; -.
DR IntAct; P0A873; 1.
DR STRING; 511145.b2607; -.
DR jPOST; P0A873; -.
DR PaxDb; P0A873; -.
DR PRIDE; P0A873; -.
DR EnsemblBacteria; AAC75656; AAC75656; b2607.
DR EnsemblBacteria; BAA16492; BAA16492; BAA16492.
DR GeneID; 66673504; -.
DR GeneID; 947099; -.
DR KEGG; ecj:JW2588; -.
DR KEGG; eco:b2607; -.
DR PATRIC; fig|1411691.4.peg.4132; -.
DR EchoBASE; EB1016; -.
DR eggNOG; COG0336; Bacteria.
DR HOGENOM; CLU_047363_0_1_6; -.
DR InParanoid; P0A873; -.
DR OMA; ILCGHYK; -.
DR PhylomeDB; P0A873; -.
DR BioCyc; EcoCyc:EG11023-MON; -.
DR BioCyc; MetaCyc:EG11023-MON; -.
DR BRENDA; 2.1.1.228; 2026.
DR EvolutionaryTrace; P0A873; -.
DR PRO; PR:P0A873; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0000287; F:magnesium ion binding; IDA:EcoCyc.
DR GO; GO:0052906; F:tRNA (guanine(37)-N(1))-methyltransferase activity; IDA:EcoCyc.
DR GO; GO:0009019; F:tRNA (guanine-N1-)-methyltransferase activity; IDA:EcoCyc.
DR GO; GO:0030488; P:tRNA methylation; IMP:EcoCyc.
DR GO; GO:0002939; P:tRNA N1-guanine methylation; IDA:EcoCyc.
DR CDD; cd18080; TrmD-like; 1.
DR DisProt; DP02716; -.
DR Gene3D; 1.10.1270.20; -; 1.
DR Gene3D; 3.40.1280.10; -; 1.
DR HAMAP; MF_00605; TrmD; 1.
DR InterPro; IPR029028; Alpha/beta_knot_MTases.
DR InterPro; IPR002649; tRNA_m1G_MeTrfase_bac.
DR InterPro; IPR023148; tRNA_m1G_MeTrfase_C_sf.
DR InterPro; IPR029026; tRNA_m1G_MTases_N.
DR InterPro; IPR016009; tRNA_MeTrfase_TRMD/TRM10.
DR PANTHER; PTHR46417; PTHR46417; 1.
DR Pfam; PF01746; tRNA_m1G_MT; 1.
DR PIRSF; PIRSF000386; tRNA_mtase; 1.
DR SUPFAM; SSF75217; SSF75217; 1.
DR TIGRFAMs; TIGR00088; trmD; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Direct protein sequencing; Methyltransferase;
KW Reference proteome; S-adenosyl-L-methionine; Transferase; tRNA processing.
FT CHAIN 1..255
FT /note="tRNA (guanine-N(1)-)-methyltransferase"
FT /id="PRO_0000060375"
FT ACT_SITE 169
FT /note="Proton acceptor"
FT /evidence="ECO:0000305|PubMed:14583191"
FT BINDING 86
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 113
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 133..138
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:14583191"
FT MUTAGEN 59
FT /note="G->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:14583191"
FT MUTAGEN 91
FT /note="G->A: Loss of activity; no effect on tRNA binding."
FT /evidence="ECO:0000269|PubMed:14583191"
FT MUTAGEN 114
FT /note="R->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:14583191"
FT MUTAGEN 115
FT /note="Y->A: Increases Km for S-adenosyl-L-methionine 24-
FT fold."
FT /evidence="ECO:0000269|PubMed:14583191"
FT MUTAGEN 117
FT /note="G->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:14583191"
FT MUTAGEN 119
FT /note="D->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:14583191"
FT MUTAGEN 121
FT /note="R->A: Loss of activity; no effect on tRNA binding."
FT /evidence="ECO:0000269|PubMed:14583191"
FT MUTAGEN 128
FT /note="D->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:14583191"
FT MUTAGEN 135
FT /note="D->A: Loss of activity; no effect on tRNA binding."
FT /evidence="ECO:0000269|PubMed:14583191"
FT MUTAGEN 136
FT /note="Y->A: Increases Km for S-adenosyl-L-methionine 68-
FT fold."
FT /evidence="ECO:0000269|PubMed:14583191"
FT MUTAGEN 141
FT /note="G->A: Increases Km for S-adenosyl-L-methionine 82-
FT fold."
FT /evidence="ECO:0000269|PubMed:14583191"
FT MUTAGEN 154
FT /note="R->A: Loss of activity; no effect on tRNA binding."
FT /evidence="ECO:0000269|PubMed:14583191"
FT MUTAGEN 169
FT /note="D->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:14583191"
FT MUTAGEN 171
FT /note="F->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:14583191"
FT MUTAGEN 184
FT /note="P->A: Loss of activity; no effect on tRNA binding."
FT /evidence="ECO:0000269|PubMed:14583191"
FT MUTAGEN 192
FT /note="V->A: Loss of activity; no effect on tRNA binding."
FT /evidence="ECO:0000269|PubMed:14583191"
FT MUTAGEN 193
FT /note="P->A: Loss of activity; no effect on tRNA binding."
FT /evidence="ECO:0000269|PubMed:14583191"
FT MUTAGEN 196
FT /note="L->A: Loss of activity; no effect on tRNA binding."
FT /evidence="ECO:0000269|PubMed:14583191"
FT MUTAGEN 197
FT /note="L->A: Loss of activity; no effect on tRNA binding."
FT /evidence="ECO:0000269|PubMed:14583191"
FT MUTAGEN 204
FT /note="I->A: Loss of activity; no effect on tRNA binding."
FT /evidence="ECO:0000269|PubMed:14583191"
FT MUTAGEN 207
FT /note="W->A: Loss of activity; no effect on tRNA binding."
FT /evidence="ECO:0000269|PubMed:14583191"
FT MUTAGEN 207
FT /note="W->F,H: Small decrease in activity."
FT /evidence="ECO:0000269|PubMed:14583191"
FT MUTAGEN 208
FT /note="R->A: Loss of activity; no effect on tRNA binding."
FT /evidence="ECO:0000269|PubMed:14583191"
FT STRAND 2..6
FT /evidence="ECO:0007829|PDB:1P9P"
FT HELIX 10..13
FT /evidence="ECO:0007829|PDB:1P9P"
FT HELIX 14..17
FT /evidence="ECO:0007829|PDB:1P9P"
FT HELIX 20..27
FT /evidence="ECO:0007829|PDB:1P9P"
FT STRAND 32..36
FT /evidence="ECO:0007829|PDB:1P9P"
FT HELIX 38..41
FT /evidence="ECO:0007829|PDB:1P9P"
FT HELIX 64..78
FT /evidence="ECO:0007829|PDB:1P9P"
FT STRAND 83..87
FT /evidence="ECO:0007829|PDB:1P9P"
FT STRAND 91..93
FT /evidence="ECO:0007829|PDB:1P9P"
FT HELIX 96..103
FT /evidence="ECO:0007829|PDB:1P9P"
FT STRAND 106..111
FT /evidence="ECO:0007829|PDB:1P9P"
FT HELIX 120..126
FT /evidence="ECO:0007829|PDB:1P9P"
FT STRAND 128..136
FT /evidence="ECO:0007829|PDB:1P9P"
FT HELIX 142..153
FT /evidence="ECO:0007829|PDB:1P9P"
FT TURN 157..159
FT /evidence="ECO:0007829|PDB:1P9P"
FT STRAND 185..187
FT /evidence="ECO:0007829|PDB:1P9P"
FT HELIX 194..197
FT /evidence="ECO:0007829|PDB:1P9P"
FT HELIX 201..219
FT /evidence="ECO:0007829|PDB:1P9P"
FT HELIX 221..225
FT /evidence="ECO:0007829|PDB:1P9P"
FT HELIX 231..245
FT /evidence="ECO:0007829|PDB:1P9P"
SQ SEQUENCE 255 AA; 28422 MW; B101087229B4CDBD CRC64;
MWIGIISLFP EMFRAITDYG VTGRAVKNGL LSIQSWSPRD FTHDRHRTVD DRPYGGGPGM
LMMVQPLRDA IHAAKAAAGE GAKVIYLSPQ GRKLDQAGVS ELATNQKLIL VCGRYEGIDE
RVIQTEIDEE WSIGDYVLSG GELPAMTLID SVSRFIPGVL GHEASATEDS FAEGLLDCPH
YTRPEVLEGM EVPPVLLSGN HAEIRRWRLK QSLGRTWLRR PELLENLALT EEQARLLAEF
KTEHAQQQHK HDGMA
