TRMR_BACSU
ID TRMR_BACSU Reviewed; 217 AA.
AC O32036;
DT 20-JAN-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 109.
DE RecName: Full=tRNA 5-hydroxyuridine methyltransferase {ECO:0000255|HAMAP-Rule:MF_02217, ECO:0000305};
DE EC=2.1.1.- {ECO:0000255|HAMAP-Rule:MF_02217, ECO:0000269|PubMed:29982645};
DE AltName: Full=ho5U methyltransferase {ECO:0000255|HAMAP-Rule:MF_02217, ECO:0000303|PubMed:29982645};
GN Name=trmR {ECO:0000255|HAMAP-Rule:MF_02217, ECO:0000303|PubMed:29982645};
GN Synonyms=yrrM; OrderedLocusNames=BSU27360;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [2] {ECO:0007744|PDB:5ZW3, ECO:0007744|PDB:5ZW4}
RP X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) IN COMPLEXES WITH
RP S-ADENOSYL-L-METHIONINE; S-ADENOSYL-L-HOMOCYSTEINE; MAGNESIUM AND ANTICODON
RP STEMLOOP OF TRNA(ALA), FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, AND
RP DISRUPTION PHENOTYPE.
RC STRAIN=168;
RX PubMed=29982645; DOI=10.1093/nar/gky592;
RA Ryu H., Grove T.L., Almo S.C., Kim J.;
RT "Identification of a novel tRNA wobble uridine modifying activity in the
RT biosynthesis of 5-methoxyuridine.";
RL Nucleic Acids Res. 46:9160-9169(2018).
CC -!- FUNCTION: Catalyzes the methylation of 5-hydroxyuridine (ho5U) to form
CC 5-methoxyuridine (mo5U) at position 34 in tRNAs. {ECO:0000255|HAMAP-
CC Rule:MF_02217, ECO:0000269|PubMed:29982645}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5-hydroxyuridine(34) in tRNA + S-adenosyl-L-methionine = 5-
CC methoxyuridine(34) in tRNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:60524, Rhea:RHEA-COMP:13381, Rhea:RHEA-COMP:15591,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:136877, ChEBI:CHEBI:143860; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_02217, ECO:0000269|PubMed:29982645};
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_02217,
CC ECO:0000269|PubMed:29982645}.
CC -!- DISRUPTION PHENOTYPE: Deletion mutant does not contain mo5U.
CC {ECO:0000269|PubMed:29982645}.
CC -!- MISCELLANEOUS: Binds magnesium, but the ion is dispensable for mo5U
CC forming activity. {ECO:0000269|PubMed:29982645}.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. Cation-dependent O-methyltransferase family.
CC {ECO:0000255|HAMAP-Rule:MF_02217}.
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DR EMBL; AL009126; CAB14678.1; -; Genomic_DNA.
DR PIR; F69979; F69979.
DR RefSeq; NP_390614.1; NC_000964.3.
DR RefSeq; WP_003229800.1; NZ_JNCM01000036.1.
DR PDB; 5ZW3; X-ray; 2.27 A; A/B=1-217.
DR PDB; 5ZW4; X-ray; 1.70 A; A=1-217.
DR PDBsum; 5ZW3; -.
DR PDBsum; 5ZW4; -.
DR AlphaFoldDB; O32036; -.
DR SMR; O32036; -.
DR STRING; 224308.BSU27360; -.
DR PaxDb; O32036; -.
DR PRIDE; O32036; -.
DR EnsemblBacteria; CAB14678; CAB14678; BSU_27360.
DR GeneID; 937719; -.
DR KEGG; bsu:BSU27360; -.
DR PATRIC; fig|224308.179.peg.2972; -.
DR eggNOG; COG4122; Bacteria.
DR InParanoid; O32036; -.
DR OMA; RGMRPDG; -.
DR PhylomeDB; O32036; -.
DR BioCyc; BSUB:BSU27360-MON; -.
DR BioCyc; MetaCyc:BSU27360-MON; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0008171; F:O-methyltransferase activity; IBA:GO_Central.
DR GO; GO:0016300; F:tRNA (uracil) methyltransferase activity; IEA:UniProtKB-UniRule.
DR Gene3D; 3.40.50.150; -; 1.
DR HAMAP; MF_02217; TrmR_methyltr; 1.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR InterPro; IPR002935; SAM_O-MeTrfase.
DR InterPro; IPR043675; TrmR_methyltr.
DR Pfam; PF01596; Methyltransf_3; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR PROSITE; PS51682; SAM_OMT_I; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Magnesium; Metal-binding; Methyltransferase;
KW Reference proteome; S-adenosyl-L-methionine; Transferase; tRNA processing.
FT CHAIN 1..217
FT /note="tRNA 5-hydroxyuridine methyltransferase"
FT /id="PRO_0000360804"
FT BINDING 38
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02217,
FT ECO:0000269|PubMed:29982645"
FT BINDING 68
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02217,
FT ECO:0000269|PubMed:29982645"
FT BINDING 85
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02217,
FT ECO:0000269|PubMed:29982645"
FT BINDING 113..114
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02217,
FT ECO:0000269|PubMed:29982645"
FT BINDING 133
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02217,
FT ECO:0000269|PubMed:29982645"
FT BINDING 133
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02217,
FT ECO:0000269|PubMed:29982645"
FT BINDING 159
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02217,
FT ECO:0000269|PubMed:29982645"
FT BINDING 160
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02217,
FT ECO:0000269|PubMed:29982645"
FT HELIX 4..15
FT /evidence="ECO:0007829|PDB:5ZW4"
FT HELIX 21..32
FT /evidence="ECO:0007829|PDB:5ZW4"
FT HELIX 40..53
FT /evidence="ECO:0007829|PDB:5ZW4"
FT STRAND 56..61
FT /evidence="ECO:0007829|PDB:5ZW4"
FT HELIX 67..75
FT /evidence="ECO:0007829|PDB:5ZW4"
FT STRAND 80..85
FT /evidence="ECO:0007829|PDB:5ZW4"
FT HELIX 88..100
FT /evidence="ECO:0007829|PDB:5ZW4"
FT TURN 104..106
FT /evidence="ECO:0007829|PDB:5ZW4"
FT STRAND 107..112
FT /evidence="ECO:0007829|PDB:5ZW4"
FT HELIX 114..116
FT /evidence="ECO:0007829|PDB:5ZW4"
FT HELIX 118..122
FT /evidence="ECO:0007829|PDB:5ZW4"
FT STRAND 127..132
FT /evidence="ECO:0007829|PDB:5ZW4"
FT HELIX 136..138
FT /evidence="ECO:0007829|PDB:5ZW4"
FT HELIX 139..146
FT /evidence="ECO:0007829|PDB:5ZW4"
FT HELIX 147..149
FT /evidence="ECO:0007829|PDB:5ZW4"
FT STRAND 150..159
FT /evidence="ECO:0007829|PDB:5ZW4"
FT HELIX 163..168
FT /evidence="ECO:0007829|PDB:5ZW4"
FT HELIX 177..195
FT /evidence="ECO:0007829|PDB:5ZW4"
FT STRAND 199..204
FT /evidence="ECO:0007829|PDB:5ZW4"
FT STRAND 210..215
FT /evidence="ECO:0007829|PDB:5ZW4"
SQ SEQUENCE 217 AA; 25063 MW; D210CC0579360F28 CRC64;
MTDRYEQIND YIEALLKPRP DNVKRLEAYA EEHHVPIMEK AGMEVLLQIL SVKQPKKILE
IGTAIGYSAI RMALELPSAE IYTIERNEKR HEEAVNNIKE FQLDDRIHVF YGDALELADA
VHVTAPYDVI FIDAAKGQYQ NFFHLYEPML SPDGVIITDN VLFKGLVAED YSKIEPKRRR
RLVAKIDEYN HWLMNHPDYQ TAIIPVGDGL AISKKKR
