TRM4_METJA
ID TRM4_METJA Reviewed; 274 AA.
AC Q60343;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 1.
DT 03-AUG-2022, entry version 109.
DE RecName: Full=tRNA (cytosine(48)-C(5))-methyltransferase;
DE EC=2.1.1.- {ECO:0000269|PubMed:20600111};
DE AltName: Full=aTrm4;
DE AltName: Full=tRNA (cytosine-5-)-methyltransferase Trm4;
GN Name=trm4; OrderedLocusNames=MJ0026;
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 X-RAY CRYSTALLOGRAPHY (1.27 ANGSTROMS) IN COMPLEX WITH SINEFUNGIN,
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=20600111; DOI=10.1016/j.jmb.2010.06.046;
RA Kuratani M., Hirano M., Goto-Ito S., Itoh Y., Hikida Y., Nishimoto M.,
RA Sekine S., Bessho Y., Ito T., Grosjean H., Yokoyama S.;
RT "Crystal structure of Methanocaldococcus jannaschii Trm4 complexed with
RT sinefungin.";
RL J. Mol. Biol. 401:323-333(2010).
CC -!- FUNCTION: Catalyzes AdoMet-dependent formation of m5C in tRNA. Cytidine
CC residue at either position 40 or position 48 is likely to be
CC methylated. {ECO:0000269|PubMed:20600111}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(48) in tRNA precursor + S-adenosyl-L-methionine = 5-
CC methylcytidine(48) in tRNA precursor + H(+) + S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:54136, Rhea:RHEA-COMP:13806, Rhea:RHEA-
CC COMP:13807, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74483, ChEBI:CHEBI:82748;
CC Evidence={ECO:0000305|PubMed:20600111};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(40) in tRNA precursor + S-adenosyl-L-methionine = 5-
CC methylcytidine(40) in tRNA precursor + H(+) + S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:42944, Rhea:RHEA-COMP:10292, Rhea:RHEA-
CC COMP:10296, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74483, ChEBI:CHEBI:82748;
CC Evidence={ECO:0000305|PubMed:20600111};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. RsmB/NOP family. {ECO:0000255|PROSITE-ProRule:PRU01023}.
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DR EMBL; L77117; AAB98007.1; -; Genomic_DNA.
DR PIR; B64303; B64303.
DR PDB; 3A4T; X-ray; 2.30 A; A/B=1-274.
DR PDB; 3AJD; X-ray; 1.27 A; A=1-274.
DR PDBsum; 3A4T; -.
DR PDBsum; 3AJD; -.
DR AlphaFoldDB; Q60343; -.
DR SMR; Q60343; -.
DR STRING; 243232.MJ_0026; -.
DR PRIDE; Q60343; -.
DR EnsemblBacteria; AAB98007; AAB98007; MJ_0026.
DR KEGG; mja:MJ_0026; -.
DR eggNOG; arCOG00973; Archaea.
DR HOGENOM; CLU_005316_7_0_2; -.
DR InParanoid; Q60343; -.
DR OMA; EPEENEF; -.
DR PhylomeDB; Q60343; -.
DR EvolutionaryTrace; Q60343; -.
DR Proteomes; UP000000805; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0016428; F:tRNA (cytosine-5-)-methyltransferase activity; IDA:UniProtKB.
DR GO; GO:0001510; P:RNA methylation; IBA:GO_Central.
DR GO; GO:0030488; P:tRNA methylation; IDA:UniProtKB.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR018314; Fmu/NOL1/Nop2p_CS.
DR InterPro; IPR001678; MeTrfase_RsmB/NOP2.
DR InterPro; IPR011023; Nop2p.
DR InterPro; IPR023267; RCMT.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR PANTHER; PTHR22807; PTHR22807; 1.
DR Pfam; PF01189; Methyltr_RsmB-F; 1.
DR PRINTS; PR02008; RCMTFAMILY.
DR SUPFAM; SSF53335; SSF53335; 1.
DR TIGRFAMs; TIGR00446; nop2p; 1.
DR PROSITE; PS01153; NOL1_NOP2_SUN; 1.
DR PROSITE; PS51686; SAM_MT_RSMB_NOP; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Methyltransferase; Reference proteome;
KW RNA-binding; S-adenosyl-L-methionine; Transferase; tRNA processing.
FT CHAIN 1..274
FT /note="tRNA (cytosine(48)-C(5))-methyltransferase"
FT /id="PRO_0000211821"
FT ACT_SITE 212
FT /note="Nucleophile"
FT /evidence="ECO:0000305"
FT BINDING 91..97
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 115
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 120
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 142
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 163
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 169
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 STRAND 11..15
FT /evidence="ECO:0007829|PDB:3AJD"
FT TURN 17..19
FT /evidence="ECO:0007829|PDB:3AJD"
FT HELIX 22..30
FT /evidence="ECO:0007829|PDB:3AJD"
FT TURN 31..33
FT /evidence="ECO:0007829|PDB:3AJD"
FT STRAND 35..38
FT /evidence="ECO:0007829|PDB:3AJD"
FT STRAND 44..49
FT /evidence="ECO:0007829|PDB:3AJD"
FT HELIX 58..61
FT /evidence="ECO:0007829|PDB:3AJD"
FT STRAND 64..67
FT /evidence="ECO:0007829|PDB:3AJD"
FT HELIX 71..73
FT /evidence="ECO:0007829|PDB:3AJD"
FT HELIX 74..79
FT /evidence="ECO:0007829|PDB:3AJD"
FT STRAND 86..89
FT /evidence="ECO:0007829|PDB:3AJD"
FT HELIX 96..104
FT /evidence="ECO:0007829|PDB:3AJD"
FT TURN 105..107
FT /evidence="ECO:0007829|PDB:3AJD"
FT STRAND 109..116
FT /evidence="ECO:0007829|PDB:3AJD"
FT HELIX 118..130
FT /evidence="ECO:0007829|PDB:3AJD"
FT STRAND 135..141
FT /evidence="ECO:0007829|PDB:3AJD"
FT HELIX 143..152
FT /evidence="ECO:0007829|PDB:3AJD"
FT STRAND 157..164
FT /evidence="ECO:0007829|PDB:3AJD"
FT HELIX 167..169
FT /evidence="ECO:0007829|PDB:3A4T"
FT HELIX 180..183
FT /evidence="ECO:0007829|PDB:3AJD"
FT HELIX 185..187
FT /evidence="ECO:0007829|PDB:3AJD"
FT HELIX 190..200
FT /evidence="ECO:0007829|PDB:3AJD"
FT STRAND 201..212
FT /evidence="ECO:0007829|PDB:3AJD"
FT HELIX 216..218
FT /evidence="ECO:0007829|PDB:3A4T"
FT HELIX 220..229
FT /evidence="ECO:0007829|PDB:3AJD"
FT STRAND 231..236
FT /evidence="ECO:0007829|PDB:3AJD"
FT STRAND 248..250
FT /evidence="ECO:0007829|PDB:3AJD"
FT STRAND 257..259
FT /evidence="ECO:0007829|PDB:3AJD"
FT STRAND 266..273
FT /evidence="ECO:0007829|PDB:3AJD"
SQ SEQUENCE 274 AA; 31490 MW; F7396827523369CF CRC64;
MMIVYKGEKM QFIRVNTLKI NPEVLKKRLE NKGVVLEKTF LDYAFEVKKS PFSIGSTPEY
LFGYYMPQSI SSMIPPIVLN PREDDFILDM CAAPGGKTTH LAQLMKNKGT IVAVEISKTR
TKALKSNINR MGVLNTIIIN ADMRKYKDYL LKNEIFFDKI LLDAPCSGNI IKDKNRNVSE
EDIKYCSLRQ KELIDIGIDL LKKDGELVYS TCSMEVEENE EVIKYILQKR NDVELIIIKA
NEFKGINIKE GYIKGTLRVF PPNEPFFIAK LRKI
