TRMY_METJA
ID TRMY_METJA Reviewed; 205 AA.
AC Q59034;
DT 25-OCT-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 106.
DE RecName: Full=tRNA (pseudouridine(54)-N(1))-methyltransferase {ECO:0000255|HAMAP-Rule:MF_00587};
DE EC=2.1.1.257 {ECO:0000255|HAMAP-Rule:MF_00587};
GN Name=trmY {ECO:0000255|HAMAP-Rule:MF_00587}; OrderedLocusNames=MJ1640;
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, AND CATALYTIC ACTIVITY.
RX PubMed=22274954; DOI=10.1261/rna.028498.111;
RA Wurm J.P., Griese M., Bahr U., Held M., Heckel A., Karas M., Soppa J.,
RA Woehnert J.;
RT "Identification of the enzyme responsible for N1-methylation of
RT pseudouridine 54 in archaeal tRNAs.";
RL RNA 18:412-420(2012).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, AND GENE NAME.
RX PubMed=22274953; DOI=10.1261/rna.030841.111;
RA Chatterjee K., Blaby I.K., Thiaville P.C., Majumder M., Grosjean H.,
RA Yuan Y.A., Gupta R., de Crecy-Lagard V.;
RT "The archaeal COG1901/DUF358 SPOUT-methyltransferase members, together with
RT pseudouridine synthase Pus10, catalyze the formation of 1-
RT methylpseudouridine at position 54 of tRNA.";
RL RNA 18:421-433(2012).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.40 ANGSTROMS) IN COMPLEX WITH
RP S-ADENOSYL-L-METHIONINE, AND SUBUNIT.
RX PubMed=21098051; DOI=10.1093/jmcb/mjq034;
RA Chen H.Y., Yuan Y.A.;
RT "Crystal structure of Mj1640/DUF358 protein reveals a putative SPOUT-class
RT RNA methyltransferase.";
RL J. Mol. Cell Biol. 2:366-374(2010).
CC -!- FUNCTION: Specifically catalyzes the N1-methylation of pseudouridine at
CC position 54 (Psi54) in tRNAs. {ECO:0000255|HAMAP-Rule:MF_00587,
CC ECO:0000269|PubMed:22274953, ECO:0000269|PubMed:22274954}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=pseudouridine(54) in tRNA + S-adenosyl-L-methionine = H(+) +
CC N(1)-methylpseudouridine(54) in tRNA + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:55292, Rhea:RHEA-COMP:14140, Rhea:RHEA-COMP:14141,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:65314, ChEBI:CHEBI:74890; EC=2.1.1.257;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00587,
CC ECO:0000269|PubMed:22274953, ECO:0000269|PubMed:22274954};
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00587,
CC ECO:0000269|PubMed:21098051}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00587}.
CC -!- SIMILARITY: Belongs to the methyltransferase superfamily. TrmY family.
CC {ECO:0000255|HAMAP-Rule:MF_00587}.
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DR EMBL; L77117; AAB99660.1; -; Genomic_DNA.
DR PIR; F64504; F64504.
DR RefSeq; WP_010871164.1; NC_000909.1.
DR PDB; 3AI9; X-ray; 1.55 A; X=1-205.
DR PDB; 3AIA; X-ray; 1.40 A; A/B=1-205.
DR PDBsum; 3AI9; -.
DR PDBsum; 3AIA; -.
DR AlphaFoldDB; Q59034; -.
DR SMR; Q59034; -.
DR STRING; 243232.MJ_1640; -.
DR EnsemblBacteria; AAB99660; AAB99660; MJ_1640.
DR GeneID; 1452549; -.
DR KEGG; mja:MJ_1640; -.
DR eggNOG; arCOG01239; Archaea.
DR HOGENOM; CLU_107018_0_0_2; -.
DR InParanoid; Q59034; -.
DR OMA; HADHCII; -.
DR OrthoDB; 126445at2157; -.
DR PhylomeDB; Q59034; -.
DR BRENDA; 2.1.1.257; 3260.
DR EvolutionaryTrace; Q59034; -.
DR Proteomes; UP000000805; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0008757; F:S-adenosylmethionine-dependent methyltransferase activity; IDA:UniProtKB.
DR GO; GO:0008175; F:tRNA methyltransferase activity; IDA:UniProtKB.
DR GO; GO:0030488; P:tRNA methylation; IDA:UniProtKB.
DR CDD; cd18087; TrmY-like; 1.
DR Gene3D; 3.40.1280.10; -; 1.
DR HAMAP; MF_00587; tRNA_methyltr_TrmY; 1.
DR InterPro; IPR029028; Alpha/beta_knot_MTases.
DR InterPro; IPR007158; TrmY.
DR InterPro; IPR029026; tRNA_m1G_MTases_N.
DR PANTHER; PTHR40703; PTHR40703; 1.
DR Pfam; PF04013; Methyltrn_RNA_2; 1.
DR SUPFAM; SSF75217; SSF75217; 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..205
FT /note="tRNA (pseudouridine(54)-N(1))-methyltransferase"
FT /id="PRO_0000157948"
FT BINDING 136
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00587,
FT ECO:0000269|PubMed:21098051"
FT BINDING 156
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00587,
FT ECO:0000269|PubMed:21098051"
FT BINDING 179..184
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 189
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00587,
FT ECO:0000269|PubMed:21098051"
FT STRAND 2..10
FT /evidence="ECO:0007829|PDB:3AIA"
FT HELIX 19..21
FT /evidence="ECO:0007829|PDB:3AIA"
FT TURN 22..27
FT /evidence="ECO:0007829|PDB:3AIA"
FT HELIX 29..40
FT /evidence="ECO:0007829|PDB:3AIA"
FT STRAND 43..46
FT /evidence="ECO:0007829|PDB:3AIA"
FT STRAND 50..56
FT /evidence="ECO:0007829|PDB:3AIA"
FT STRAND 59..61
FT /evidence="ECO:0007829|PDB:3AIA"
FT STRAND 64..69
FT /evidence="ECO:0007829|PDB:3AIA"
FT TURN 70..72
FT /evidence="ECO:0007829|PDB:3AIA"
FT HELIX 80..96
FT /evidence="ECO:0007829|PDB:3AIA"
FT HELIX 101..103
FT /evidence="ECO:0007829|PDB:3AIA"
FT STRAND 106..109
FT /evidence="ECO:0007829|PDB:3AIA"
FT STRAND 112..115
FT /evidence="ECO:0007829|PDB:3AIA"
FT HELIX 119..128
FT /evidence="ECO:0007829|PDB:3AIA"
FT STRAND 132..136
FT /evidence="ECO:0007829|PDB:3AIA"
FT STRAND 140..142
FT /evidence="ECO:0007829|PDB:3AIA"
FT HELIX 143..145
FT /evidence="ECO:0007829|PDB:3AIA"
FT STRAND 150..156
FT /evidence="ECO:0007829|PDB:3AIA"
FT HELIX 163..171
FT /evidence="ECO:0007829|PDB:3AIA"
FT STRAND 175..178
FT /evidence="ECO:0007829|PDB:3AIA"
FT HELIX 186..199
FT /evidence="ECO:0007829|PDB:3AIA"
SQ SEQUENCE 205 AA; 23704 MW; EBED16985B07E132 CRC64;
MREFIFKANK TITSSDINLK DLPGSCGRLD LLCRCVSDAF FLSHDIRRDV VFYAVLYGQP
NPPVCIKFVG SELKKVSPDE RNIAIFIKKA LKKFEELDEE QRKDWNQSTP GIYVRRLGFR
NLVLEKLEEG KNIYYLHMNG EDVENVDIEN PVFIIGDHIG IGEEDERFLD EIKAKRISLS
PLELHANHCI TIIHNVLDKK RICEI
