TRM5B_METJA
ID TRM5B_METJA Reviewed; 336 AA.
AC Q58293;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 110.
DE RecName: Full=tRNA (guanine(37)-N1)-methyltransferase Trm5b;
DE EC=2.1.1.228 {ECO:0000269|PubMed:15165845};
DE AltName: Full=M1G-methyltransferase;
DE AltName: Full=tRNA [GM37] methyltransferase;
GN Name=trm5b; OrderedLocusNames=MJ0883;
OS Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM
OS 10045 / NBRC 100440) (Methanococcus jannaschii).
OC Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC Methanocaldococcaceae; Methanocaldococcus.
OX NCBI_TaxID=243232;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=8688087; DOI=10.1126/science.273.5278.1058;
RA Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G.,
RA Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R.,
RA Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R.,
RA Kirkness E.F., Weinstock K.G., Merrick J.M., Glodek A., Scott J.L.,
RA Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D., Utterback T.R.,
RA Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C., Cotton M.D.,
RA Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M., Klenk H.-P.,
RA Fraser C.M., Smith H.O., Woese C.R., Venter J.C.;
RT "Complete genome sequence of the methanogenic archaeon, Methanococcus
RT jannaschii.";
RL Science 273:1058-1073(1996).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, AND SUBUNIT.
RX PubMed=15165845; DOI=10.1016/j.jmb.2004.04.025;
RA Christian T., Evilia C., Williams S., Hou Y.M.;
RT "Distinct origins of tRNA(m1G37) methyltransferase.";
RL J. Mol. Biol. 339:707-719(2004).
RN [3]
RP FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, AND MUTAGENESIS OF ARG-145;
RP TYR-177; GLY-205; GLY-207; ASP-223; ASN-225; PRO-226; ASN-265 AND PRO-267.
RX PubMed=16768442; DOI=10.1021/bi0602314;
RA Christian T., Evilia C., Hou Y.M.;
RT "Catalysis by the second class of tRNA(m1G37) methyl transferase requires a
RT conserved proline.";
RL Biochemistry 45:7463-7473(2006).
RN [4]
RP FUNCTION.
RX PubMed=20980671; DOI=10.1261/rna.2376210;
RA Christian T., Lahoud G., Liu C., Hoffmann K., Perona J.J., Hou Y.M.;
RT "Mechanism of N-methylation by the tRNA m1G37 methyltransferase Trm5.";
RL RNA 16:2484-2492(2010).
RN [5] {ECO:0007744|PDB:2YX1}
RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS), AND SUBUNIT.
RX PubMed=18384044; DOI=10.1002/prot.22019;
RA Goto-Ito S., Ito T., Ishii R., Muto Y., Bessho Y., Yokoyama S.;
RT "Crystal structure of archaeal tRNA(m(1)G37)methyltransferase aTrm5.";
RL Proteins 72:1274-1289(2008).
RN [6] {ECO:0007744|PDB:2ZZM, ECO:0007744|PDB:2ZZN}
RP X-RAY CRYSTALLOGRAPHY (2.65 ANGSTROMS) IN COMPLEX WITH
RP S-ADENOSYL-L-METHIONINE AND TRNA.
RX PubMed=19749755; DOI=10.1038/nsmb.1653;
RA Goto-Ito S., Ito T., Kuratani M., Bessho Y., Yokoyama S.;
RT "Tertiary structure checkpoint at anticodon loop modification in tRNA
RT functional maturation.";
RL Nat. Struct. Mol. Biol. 16:1109-1115(2009).
CC -!- FUNCTION: Specifically methylates the N1 position of guanosine-37 in
CC various tRNAs. {ECO:0000269|PubMed:15165845,
CC ECO:0000269|PubMed:16768442, ECO:0000269|PubMed:20980671}.
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:15165845};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.0 uM for S-adenosyl-L-methionine {ECO:0000269|PubMed:16768442};
CC KM=0.7 uM for tRNA {ECO:0000269|PubMed:16768442};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:15165845,
CC ECO:0000269|PubMed:18384044, ECO:0000269|PubMed:19749755}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. TRM5/TYW2 family. {ECO:0000255|PROSITE-ProRule:PRU01021}.
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DR EMBL; L77117; AAB98887.1; -; Genomic_DNA.
DR PIR; C64410; C64410.
DR RefSeq; WP_010870397.1; NC_000909.1.
DR PDB; 2YX1; X-ray; 2.20 A; A/B=1-336.
DR PDB; 2ZZM; X-ray; 2.65 A; A=1-336.
DR PDB; 2ZZN; X-ray; 2.95 A; A/B=1-336.
DR PDB; 3AY0; X-ray; 3.05 A; A/B=1-336.
DR PDBsum; 2YX1; -.
DR PDBsum; 2ZZM; -.
DR PDBsum; 2ZZN; -.
DR PDBsum; 3AY0; -.
DR AlphaFoldDB; Q58293; -.
DR SMR; Q58293; -.
DR STRING; 243232.MJ_0883; -.
DR EnsemblBacteria; AAB98887; AAB98887; MJ_0883.
DR GeneID; 1451772; -.
DR KEGG; mja:MJ_0883; -.
DR eggNOG; arCOG00033; Archaea.
DR HOGENOM; CLU_022610_0_1_2; -.
DR InParanoid; Q58293; -.
DR OMA; HYYDIQH; -.
DR OrthoDB; 55502at2157; -.
DR PhylomeDB; Q58293; -.
DR BRENDA; 2.1.1.228; 3260.
DR SABIO-RK; Q58293; -.
DR EvolutionaryTrace; Q58293; -.
DR PRO; PR:Q58293; -.
DR Proteomes; UP000000805; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0052906; F:tRNA (guanine(37)-N(1))-methyltransferase activity; IEA:UniProtKB-EC.
DR GO; GO:0009019; F:tRNA (guanine-N1-)-methyltransferase activity; IDA:UniProtKB.
DR GO; GO:0008175; F:tRNA methyltransferase activity; IBA:GO_Central.
DR GO; GO:0030488; P:tRNA methylation; IDA:UniProtKB.
DR GO; GO:0002939; P:tRNA N1-guanine methylation; IBA:GO_Central.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR030382; MeTrfase_TRM5/TYW2.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR InterPro; IPR040601; Trm5_N.
DR Pfam; PF02475; Met_10; 1.
DR Pfam; PF18093; Trm5_N; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR PROSITE; PS51684; SAM_MT_TRM5_TYW2; 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..336
FT /note="tRNA (guanine(37)-N1)-methyltransferase Trm5b"
FT /id="PRO_0000107090"
FT BINDING 186
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01021,
FT ECO:0000269|PubMed:19749755"
FT BINDING 223..224
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01021,
FT ECO:0000269|PubMed:19749755"
FT BINDING 251..252
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01021,
FT ECO:0000269|PubMed:19749755"
FT BINDING 265
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01021,
FT ECO:0000269|PubMed:19749755"
FT MUTAGEN 145
FT /note="R->A: 16-fold decrease in methyltransferase
FT activity. Lack of tRNA-binding."
FT /evidence="ECO:0000269|PubMed:16768442"
FT MUTAGEN 177
FT /note="Y->A: 20-fold decrease in methyltransferase
FT activity. Reduced affinity for tRNA."
FT /evidence="ECO:0000269|PubMed:16768442"
FT MUTAGEN 205
FT /note="G->A: 33-fold decrease in methyltransferase activity
FT and reduced affinity for tRNA; when associated with A-207."
FT /evidence="ECO:0000269|PubMed:16768442"
FT MUTAGEN 207
FT /note="G->A: 33-fold decrease in methyltransferase activity
FT and reduced affinity for tRNA; when associated with A-205."
FT /evidence="ECO:0000269|PubMed:16768442"
FT MUTAGEN 223
FT /note="D->A: 100-fold decrease in methyltransferase
FT activity. Lack of tRNA-binding."
FT /evidence="ECO:0000269|PubMed:16768442"
FT MUTAGEN 225
FT /note="N->A: 20-fold decrease in methyltransferase
FT activity."
FT /evidence="ECO:0000269|PubMed:16768442"
FT MUTAGEN 226
FT /note="P->A: 16-fold decrease in methyltransferase
FT activity."
FT /evidence="ECO:0000269|PubMed:16768442"
FT MUTAGEN 265
FT /note="N->A,Q: 100-fold decrease in methyltransferase
FT activity."
FT /evidence="ECO:0000269|PubMed:16768442"
FT MUTAGEN 265
FT /note="N->H: 3-fold decrease in methyltransferase
FT activity."
FT /evidence="ECO:0000269|PubMed:16768442"
FT MUTAGEN 267
FT /note="P->A: 1000-fold decrease in methyltransferase
FT activity. No change in affinity for tRNA."
FT /evidence="ECO:0000269|PubMed:16768442"
FT STRAND 3..8
FT /evidence="ECO:0007829|PDB:2YX1"
FT HELIX 9..11
FT /evidence="ECO:0007829|PDB:2YX1"
FT HELIX 12..21
FT /evidence="ECO:0007829|PDB:2YX1"
FT STRAND 27..29
FT /evidence="ECO:0007829|PDB:2ZZM"
FT STRAND 32..34
FT /evidence="ECO:0007829|PDB:2YX1"
FT STRAND 37..42
FT /evidence="ECO:0007829|PDB:2YX1"
FT HELIX 47..50
FT /evidence="ECO:0007829|PDB:2YX1"
FT TURN 51..53
FT /evidence="ECO:0007829|PDB:2YX1"
FT STRAND 59..62
FT /evidence="ECO:0007829|PDB:2YX1"
FT HELIX 77..83
FT /evidence="ECO:0007829|PDB:2YX1"
FT HELIX 85..88
FT /evidence="ECO:0007829|PDB:2YX1"
FT STRAND 91..93
FT /evidence="ECO:0007829|PDB:2YX1"
FT STRAND 98..100
FT /evidence="ECO:0007829|PDB:2YX1"
FT STRAND 103..106
FT /evidence="ECO:0007829|PDB:2YX1"
FT STRAND 110..112
FT /evidence="ECO:0007829|PDB:3AY0"
FT HELIX 114..127
FT /evidence="ECO:0007829|PDB:2YX1"
FT STRAND 131..136
FT /evidence="ECO:0007829|PDB:2YX1"
FT TURN 142..145
FT /evidence="ECO:0007829|PDB:2ZZM"
FT STRAND 149..154
FT /evidence="ECO:0007829|PDB:2YX1"
FT STRAND 159..164
FT /evidence="ECO:0007829|PDB:2YX1"
FT STRAND 167..172
FT /evidence="ECO:0007829|PDB:2YX1"
FT TURN 173..175
FT /evidence="ECO:0007829|PDB:2YX1"
FT HELIX 180..182
FT /evidence="ECO:0007829|PDB:2YX1"
FT HELIX 183..192
FT /evidence="ECO:0007829|PDB:2YX1"
FT STRAND 198..201
FT /evidence="ECO:0007829|PDB:2YX1"
FT HELIX 208..212
FT /evidence="ECO:0007829|PDB:2YX1"
FT TURN 213..215
FT /evidence="ECO:0007829|PDB:2YX1"
FT STRAND 216..224
FT /evidence="ECO:0007829|PDB:2YX1"
FT HELIX 226..238
FT /evidence="ECO:0007829|PDB:2YX1"
FT TURN 242..244
FT /evidence="ECO:0007829|PDB:2YX1"
FT STRAND 245..250
FT /evidence="ECO:0007829|PDB:2YX1"
FT HELIX 252..254
FT /evidence="ECO:0007829|PDB:2YX1"
FT STRAND 259..264
FT /evidence="ECO:0007829|PDB:2YX1"
FT TURN 267..269
FT /evidence="ECO:0007829|PDB:2YX1"
FT HELIX 270..273
FT /evidence="ECO:0007829|PDB:2YX1"
FT HELIX 274..280
FT /evidence="ECO:0007829|PDB:2YX1"
FT STRAND 281..296
FT /evidence="ECO:0007829|PDB:2YX1"
FT HELIX 297..306
FT /evidence="ECO:0007829|PDB:2YX1"
FT STRAND 307..321
FT /evidence="ECO:0007829|PDB:2YX1"
FT STRAND 324..335
FT /evidence="ECO:0007829|PDB:2YX1"
SQ SEQUENCE 336 AA; 39000 MW; 3E4811F0932EE95F CRC64;
MPLCLKINKK HGEQTRRILI ENNLLNKDYK ITSEGNYLYL PIKDVDEDIL KSILNIEFEL
VDKELEEKKI IKKPSFREII SKKYRKEIDE GLISLSYDVV GDLVILQISD EVDEKIRKEI
GELAYKLIPC KGVFRRKSEV KGEFRVRELE HLAGENRTLT IHKENGYRLW VDIAKVYFSP
RLGGERARIM KKVSLNDVVV DMFAGVGPFS IACKNAKKIY AIDINPHAIE LLKKNIKLNK
LEHKIIPILS DVREVDVKGN RVIMNLPKFA HKFIDKALDI VEEGGVIHYY TIGKDFDKAI
KLFEKKCDCE VLEKRIVKSY APREYILALD FKINKK
