TRMJ_ECOLI
ID TRMJ_ECOLI Reviewed; 246 AA.
AC P0AE01; P76993; P77438;
DT 06-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT 06-DEC-2005, sequence version 1.
DT 03-AUG-2022, entry version 117.
DE RecName: Full=tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ {ECO:0000305};
DE EC=2.1.1.200 {ECO:0000269|PubMed:16848900, ECO:0000269|PubMed:24951554, ECO:0000269|PubMed:26202969};
DE AltName: Full=TrMet(Xm32) {ECO:0000303|PubMed:16848900};
DE AltName: Full=tRNA (cytidine(32)/uridine(32)-2'-O)-methyltransferase {ECO:0000305};
DE AltName: Full=tRNA Cm32/Um32 methyltransferase {ECO:0000305};
GN Name=trmJ {ECO:0000303|PubMed:16848900}; Synonyms=yfhQ;
GN OrderedLocusNames=b2532, JW2516;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
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 [2]
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 [3]
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 [4]
RP FUNCTION, CATALYTIC ACTIVITY, AND SUBUNIT.
RX PubMed=16848900; DOI=10.1186/1471-2199-7-23;
RA Purta E., van Vliet F., Tkaczuk K.L., Dunin-Horkawicz S., Mori H.,
RA Droogmans L., Bujnicki J.M.;
RT "The yfhQ gene of Escherichia coli encodes a tRNA:Cm32/Um32
RT methyltransferase.";
RL BMC Mol. Biol. 7:23-23(2006).
RN [5] {ECO:0007744|PDB:4CND, ECO:0007744|PDB:4CNE}
RP X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) IN COMPLEX WITH
RP S-ADENOSYL-L-HOMOCYSTEINE, FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, AND
RP MUTAGENESIS OF ARG-23 AND TYR-140.
RX PubMed=24951554; DOI=10.1261/rna.044503.114;
RA Somme J., Van Laer B., Roovers M., Steyaert J., Versees W., Droogmans L.;
RT "Characterization of two homologous 2'-O-methyltransferases showing
RT different specificities for their tRNA substrates.";
RL RNA 20:1257-1271(2014).
RN [6] {ECO:0007744|PDB:4XBO}
RP X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) IN COMPLEX WITH
RP S-ADENOSYL-L-HOMOCYSTEINE, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, SUBUNIT, DOMAIN, AND MUTAGENESIS OF ARG-82; ARG-84; ARG-115;
RP HIS-172; THR-175; TYR-177; PHE-199; LYS-211; ARG-213; ARG-214; ARG-218;
RP GLU-225; ILE-228; LEU-229 AND GLY-231.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=26202969; DOI=10.1093/nar/gkv745;
RA Liu R.J., Long T., Zhou M., Zhou X.L., Wang E.D.;
RT "tRNA recognition by a bacterial tRNA Xm32 modification enzyme from the
RT SPOUT methyltransferase superfamily.";
RL Nucleic Acids Res. 43:7489-7503(2015).
CC -!- FUNCTION: Catalyzes the formation of 2'O-methylated cytidine (Cm32) or
CC 2'O-methylated uridine (Um32) at position 32 in tRNA (PubMed:16848900,
CC PubMed:24951554, PubMed:26202969). Can also methylate adenosine or
CC guanosine, even though these nucleosides are rare or absent at position
CC 32 in the anticodon loop of tRNA (PubMed:24951554).
CC {ECO:0000269|PubMed:16848900, ECO:0000269|PubMed:24951554,
CC ECO:0000269|PubMed:26202969}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(32) in tRNA + S-adenosyl-L-methionine = 2'-O-
CC methylcytidine(32) in tRNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:42932, Rhea:RHEA-COMP:10288, Rhea:RHEA-COMP:10289,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74495, ChEBI:CHEBI:82748; EC=2.1.1.200;
CC Evidence={ECO:0000269|PubMed:16848900, ECO:0000269|PubMed:24951554,
CC ECO:0000269|PubMed:26202969};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=S-adenosyl-L-methionine + uridine(32) in tRNA = 2'-O-
CC methyluridine(32) in tRNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:42936, Rhea:RHEA-COMP:10107, Rhea:RHEA-COMP:10290,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:65315, ChEBI:CHEBI:74478; EC=2.1.1.200;
CC Evidence={ECO:0000269|PubMed:16848900, ECO:0000269|PubMed:24951554,
CC ECO:0000269|PubMed:26202969};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.67 uM for tRNA(fMet1) {ECO:0000269|PubMed:26202969};
CC KM=0.81 uM for tRNA(fMet2) {ECO:0000269|PubMed:26202969};
CC KM=0.94 uM for tRNA(Trp1) {ECO:0000269|PubMed:26202969};
CC KM=9.88 uM for tRNA(Gln1) {ECO:0000269|PubMed:26202969};
CC KM=5.79 uM for tRNA(Gln2) {ECO:0000269|PubMed:26202969};
CC KM=11.82 uM for tRNA(Ser1) {ECO:0000269|PubMed:26202969};
CC Note=kcat is 1.52 min(-1) with tRNA(fMet1) as substrate. kcat is 1.42
CC min(-1) with tRNA(fMet2) as substrate. kcat is 1.31 min(-1) with
CC tRNA(Trp1) as substrate. kcat is 1.20 min(-1) with tRNA(Gln1) as
CC substrate. kcat is 1.41 min(-1) with tRNA(Gln2) as substrate. kcat is
CC 2.30 min(-1) with tRNA(Ser1) as substrate.
CC {ECO:0000269|PubMed:26202969};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:16848900,
CC ECO:0000269|PubMed:24951554, ECO:0000269|PubMed:26202969}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- DOMAIN: Both the catalytic N-terminal domain and the extensional C-
CC terminal domain play key roles in tRNA binding and methylation.
CC {ECO:0000269|PubMed:26202969}.
CC -!- SIMILARITY: Belongs to the class IV-like SAM-binding methyltransferase
CC superfamily. RNA methyltransferase TrmH family. {ECO:0000305}.
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DR EMBL; U00096; AAC75585.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA16426.1; -; Genomic_DNA.
DR PIR; C65030; C65030.
DR RefSeq; NP_417027.1; NC_000913.3.
DR RefSeq; WP_000940019.1; NZ_SSZK01000005.1.
DR PDB; 4CND; X-ray; 1.50 A; A/B=1-246.
DR PDB; 4CNE; X-ray; 1.90 A; A/B=1-246.
DR PDB; 4XBO; X-ray; 2.60 A; A/B=1-246.
DR PDBsum; 4CND; -.
DR PDBsum; 4CNE; -.
DR PDBsum; 4XBO; -.
DR AlphaFoldDB; P0AE01; -.
DR SMR; P0AE01; -.
DR BioGRID; 4263050; 19.
DR BioGRID; 852903; 1.
DR IntAct; P0AE01; 3.
DR STRING; 511145.b2532; -.
DR jPOST; P0AE01; -.
DR PaxDb; P0AE01; -.
DR PRIDE; P0AE01; -.
DR EnsemblBacteria; AAC75585; AAC75585; b2532.
DR EnsemblBacteria; BAA16426; BAA16426; BAA16426.
DR GeneID; 58390231; -.
DR GeneID; 948610; -.
DR KEGG; ecj:JW2516; -.
DR KEGG; eco:b2532; -.
DR PATRIC; fig|511145.12.peg.2633; -.
DR EchoBASE; EB3225; -.
DR eggNOG; COG0565; Bacteria.
DR HOGENOM; CLU_056931_0_1_6; -.
DR InParanoid; P0AE01; -.
DR OMA; PIMNLSH; -.
DR PhylomeDB; P0AE01; -.
DR BioCyc; EcoCyc:G7327-MON; -.
DR BioCyc; MetaCyc:G7327-MON; -.
DR BRENDA; 2.1.1.200; 2026.
DR PRO; PR:P0AE01; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR GO; GO:0052666; F:tRNA (cytosine-2'-O-)-methyltransferase activity; IMP:EcoCyc.
DR GO; GO:0052665; F:tRNA (uracil-2'-O-)-methyltransferase activity; IMP:EcoCyc.
DR GO; GO:0002128; P:tRNA nucleoside ribose methylation; IMP:EcoCyc.
DR Gene3D; 3.40.1280.10; -; 1.
DR InterPro; IPR029028; Alpha/beta_knot_MTases.
DR InterPro; IPR004384; RNA_MeTrfase_TrmJ/LasT.
DR InterPro; IPR001537; SpoU_MeTrfase.
DR InterPro; IPR029026; tRNA_m1G_MTases_N.
DR PANTHER; PTHR42786; PTHR42786; 1.
DR Pfam; PF00588; SpoU_methylase; 1.
DR PIRSF; PIRSF004808; LasT; 1.
DR SUPFAM; SSF75217; SSF75217; 1.
DR TIGRFAMs; TIGR00050; rRNA_methyl_1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Methyltransferase; Reference proteome;
KW S-adenosyl-L-methionine; Transferase; tRNA processing.
FT CHAIN 1..246
FT /note="tRNA (cytidine/uridine-2'-O-)-methyltransferase
FT TrmJ"
FT /id="PRO_0000159824"
FT BINDING 79..81
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000305|PubMed:24951554,
FT ECO:0000305|PubMed:26202969"
FT BINDING 114
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000305|PubMed:24951554,
FT ECO:0000305|PubMed:26202969"
FT BINDING 134
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000305|PubMed:24951554,
FT ECO:0000305|PubMed:26202969"
FT BINDING 141..143
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000305|PubMed:24951554,
FT ECO:0000305|PubMed:26202969"
FT MUTAGEN 23
FT /note="R->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:24951554"
FT MUTAGEN 82
FT /note="R->A: Loss of tRNA binding affinity. Loss of
FT activity."
FT /evidence="ECO:0000269|PubMed:26202969"
FT MUTAGEN 84
FT /note="R->A: Loss of tRNA binding affinity. Loss of
FT activity."
FT /evidence="ECO:0000269|PubMed:26202969"
FT MUTAGEN 115
FT /note="R->A: No change in tRNA binding affinity. No change
FT in activity."
FT /evidence="ECO:0000269|PubMed:26202969"
FT MUTAGEN 140
FT /note="Y->F: Strong decrease in activity."
FT /evidence="ECO:0000269|PubMed:24951554"
FT MUTAGEN 172
FT /note="H->A: No change in activity."
FT /evidence="ECO:0000269|PubMed:26202969"
FT MUTAGEN 175
FT /note="T->A: No change in activity."
FT /evidence="ECO:0000269|PubMed:26202969"
FT MUTAGEN 177
FT /note="Y->A: No change in activity."
FT /evidence="ECO:0000269|PubMed:26202969"
FT MUTAGEN 199
FT /note="F->A: Strong decrease in activity."
FT /evidence="ECO:0000269|PubMed:26202969"
FT MUTAGEN 211
FT /note="K->A: Strong decrease in tRNA binding affinity.
FT Strong decrease in activity."
FT /evidence="ECO:0000269|PubMed:26202969"
FT MUTAGEN 213
FT /note="R->A: Strong decrease in tRNA binding affinity. Loss
FT of activity."
FT /evidence="ECO:0000269|PubMed:26202969"
FT MUTAGEN 214
FT /note="R->A: Strong decrease in tRNA binding affinity.
FT Strong decrease in activity."
FT /evidence="ECO:0000269|PubMed:26202969"
FT MUTAGEN 218
FT /note="R->A: Strong decrease in tRNA binding affinity.
FT Strong decrease in activity."
FT /evidence="ECO:0000269|PubMed:26202969"
FT MUTAGEN 225
FT /note="E->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:26202969"
FT MUTAGEN 228
FT /note="I->A: Strong decrease in activity."
FT /evidence="ECO:0000269|PubMed:26202969"
FT MUTAGEN 229
FT /note="L->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:26202969"
FT MUTAGEN 231
FT /note="G->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:26202969"
FT HELIX 2..4
FT /evidence="ECO:0007829|PDB:4XBO"
FT STRAND 5..11
FT /evidence="ECO:0007829|PDB:4CND"
FT HELIX 15..27
FT /evidence="ECO:0007829|PDB:4CND"
FT STRAND 32..37
FT /evidence="ECO:0007829|PDB:4CND"
FT HELIX 44..50
FT /evidence="ECO:0007829|PDB:4CND"
FT HELIX 51..53
FT /evidence="ECO:0007829|PDB:4CND"
FT HELIX 54..58
FT /evidence="ECO:0007829|PDB:4CND"
FT STRAND 61..64
FT /evidence="ECO:0007829|PDB:4CND"
FT HELIX 66..70
FT /evidence="ECO:0007829|PDB:4CND"
FT STRAND 74..79
FT /evidence="ECO:0007829|PDB:4CND"
FT STRAND 84..86
FT /evidence="ECO:0007829|PDB:4CND"
FT HELIX 93..104
FT /evidence="ECO:0007829|PDB:4CND"
FT STRAND 109..113
FT /evidence="ECO:0007829|PDB:4CND"
FT TURN 116..118
FT /evidence="ECO:0007829|PDB:4CND"
FT HELIX 122..125
FT /evidence="ECO:0007829|PDB:4CND"
FT STRAND 129..132
FT /evidence="ECO:0007829|PDB:4CND"
FT HELIX 145..162
FT /evidence="ECO:0007829|PDB:4CND"
FT HELIX 180..196
FT /evidence="ECO:0007829|PDB:4XBO"
FT HELIX 207..218
FT /evidence="ECO:0007829|PDB:4XBO"
FT HELIX 223..237
FT /evidence="ECO:0007829|PDB:4XBO"
SQ SEQUENCE 246 AA; 27048 MW; 83C1AE4507E097D2 CRC64;
MLQNIRIVLV ETSHTGNMGS VARAMKTMGL TNLWLVNPLV KPDSQAIALA AGASDVIGNA
HIVDTLDEAL AGCSLVVGTS ARSRTLPWPM LDPRECGLKS VAEAANTPVA LVFGRERVGL
TNEELQKCHY HVAIAANPEY SSLNLAMAVQ VIAYEVRMAW LATQENGEQV EHEETPYPLV
DDLERFYGHL EQTLLATGFI RENHPGQVMN KLRRLFTRAR PESQELNILR GILASIEQQN
KGNKAE
