TRM56_PYRHO
ID TRM56_PYRHO Reviewed; 203 AA.
AC O58214;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 29-AUG-2001, sequence version 2.
DT 03-AUG-2022, entry version 116.
DE RecName: Full=tRNA (cytidine(56)-2'-O)-methyltransferase;
DE EC=2.1.1.206;
DE AltName: Full=tRNA ribose 2'-O-methyltransferase aTrm56;
GN OrderedLocusNames=PH0461;
OS Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC
OS 100139 / OT-3).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=70601;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=9679194; DOI=10.1093/dnares/5.2.55;
RA Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S.,
RA Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K.,
RA Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T., Tanaka T.,
RA Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Yoshizawa T.,
RA Nakamura Y., Robb F.T., Horikoshi K., Masuchi Y., Shizuya H., Kikuchi H.;
RT "Complete sequence and gene organization of the genome of a hyper-
RT thermophilic archaebacterium, Pyrococcus horikoshii OT3.";
RL DNA Res. 5:55-76(1998).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.48 ANGSTROMS) OF 1-195 IN COMPLEX WITH
RP S-ADENOSYL-L-METHIONINE, FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, AND
RP MUTAGENESIS OF ARG-16; HIS-20; ARG-26 AND GLU-111.
RX PubMed=18068186; DOI=10.1016/j.jmb.2007.11.023;
RA Kuratani M., Bessho Y., Nishimoto M., Grosjean H., Yokoyama S.;
RT "Crystal structure and mutational study of a unique SpoU family archaeal
RT methylase that forms 2'-O-methylcytidine at position 56 of tRNA.";
RL J. Mol. Biol. 375:1064-1075(2008).
CC -!- FUNCTION: Specifically catalyzes the AdoMet-dependent 2'-O-ribose
CC methylation of cytidine at position 56 in tRNAs.
CC {ECO:0000269|PubMed:18068186}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(56) in tRNA + S-adenosyl-L-methionine = 2'-O-
CC methylcytidine(56) in tRNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:42968, Rhea:RHEA-COMP:10308, Rhea:RHEA-COMP:10309,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74495, ChEBI:CHEBI:82748; EC=2.1.1.206;
CC Evidence={ECO:0000269|PubMed:18068186};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:18068186}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the aTrm56 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAA29547.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; BA000001; BAA29547.1; ALT_INIT; Genomic_DNA.
DR PIR; F71157; F71157.
DR RefSeq; WP_048053133.1; NC_000961.1.
DR PDB; 2YY8; X-ray; 2.48 A; A/B=1-195.
DR PDBsum; 2YY8; -.
DR AlphaFoldDB; O58214; -.
DR SMR; O58214; -.
DR STRING; 70601.3256864; -.
DR EnsemblBacteria; BAA29547; BAA29547; BAA29547.
DR GeneID; 1444355; -.
DR KEGG; pho:PH0461; -.
DR eggNOG; arCOG01857; Archaea.
DR OMA; VVHLTMY; -.
DR OrthoDB; 83050at2157; -.
DR BRENDA; 2.1.1.206; 5244.
DR EvolutionaryTrace; O58214; -.
DR Proteomes; UP000000752; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0008175; F:tRNA methyltransferase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0002128; P:tRNA nucleoside ribose methylation; IEA:UniProtKB-UniRule.
DR Gene3D; 3.40.1280.10; -; 1.
DR HAMAP; MF_00077; tRNA_methyltr_aTrm56; 1.
DR InterPro; IPR029028; Alpha/beta_knot_MTases.
DR InterPro; IPR029026; tRNA_m1G_MTases_N.
DR InterPro; IPR002845; tRNA_mtfrase_aTrm56.
DR PANTHER; PTHR42197; PTHR42197; 1.
DR Pfam; PF01994; Trm56; 1.
DR PIRSF; PIRSF016123; UCP016123; 1.
DR SUPFAM; SSF75217; SSF75217; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Methyltransferase; S-adenosyl-L-methionine;
KW Transferase; tRNA processing.
FT CHAIN 1..203
FT /note="tRNA (cytidine(56)-2'-O)-methyltransferase"
FT /id="PRO_0000146935"
FT REGION 178..203
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 80
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:18068186"
FT BINDING 109..113
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 127..134
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT MUTAGEN 16
FT /note="R->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:18068186"
FT MUTAGEN 20
FT /note="H->A: Reduced enzyme activity."
FT /evidence="ECO:0000269|PubMed:18068186"
FT MUTAGEN 26
FT /note="R->A: No effect on enzyme activity."
FT /evidence="ECO:0000269|PubMed:18068186"
FT MUTAGEN 111
FT /note="E->A: Reduced enzyme activity."
FT /evidence="ECO:0000269|PubMed:18068186"
FT STRAND 2..6
FT /evidence="ECO:0007829|PDB:2YY8"
FT HELIX 16..27
FT /evidence="ECO:0007829|PDB:2YY8"
FT STRAND 31..38
FT /evidence="ECO:0007829|PDB:2YY8"
FT HELIX 41..54
FT /evidence="ECO:0007829|PDB:2YY8"
FT HELIX 66..72
FT /evidence="ECO:0007829|PDB:2YY8"
FT STRAND 75..80
FT /evidence="ECO:0007829|PDB:2YY8"
FT STRAND 84..86
FT /evidence="ECO:0007829|PDB:2YY8"
FT HELIX 87..99
FT /evidence="ECO:0007829|PDB:2YY8"
FT STRAND 104..108
FT /evidence="ECO:0007829|PDB:2YY8"
FT HELIX 115..120
FT /evidence="ECO:0007829|PDB:2YY8"
FT STRAND 122..130
FT /evidence="ECO:0007829|PDB:2YY8"
FT HELIX 134..145
FT /evidence="ECO:0007829|PDB:2YY8"
FT TURN 146..148
FT /evidence="ECO:0007829|PDB:2YY8"
FT HELIX 149..152
FT /evidence="ECO:0007829|PDB:2YY8"
FT STRAND 159..162
FT /evidence="ECO:0007829|PDB:2YY8"
FT STRAND 166..168
FT /evidence="ECO:0007829|PDB:2YY8"
FT STRAND 171..173
FT /evidence="ECO:0007829|PDB:2YY8"
SQ SEQUENCE 203 AA; 22767 MW; E81C17F5848D3414 CRC64;
MIVVLRLGHR PERDKRVTTH VALTARAFGA DGIIIASEED EKVKESVEDV VKRWGGPFFI
EFNRNWRKVM KEFTGVKVHL TMYGLHVDDV IEELKEKLKK GEDFMIIVGA EKVPREVYEL
ADYNVAIGNQ PHSEVAALAV LLDRLLEGKG LKKEFKGAKI KIVPQARGKK VVEVQGYAEQ
DKAEGKATPG KNWENSGFTG DNP
