ID   TRM2B_PONAB             Reviewed;         486 AA.
AC   Q5RFM7;
DT   04-DEC-2007, integrated into UniProtKB/Swiss-Prot.
DT   21-DEC-2004, sequence version 1.
DT   03-AUG-2022, entry version 76.
DE   RecName: Full=tRNA (uracil-5-)-methyltransferase homolog B;
DE            EC=2.1.1.35 {ECO:0000250|UniProtKB:Q96GJ1};
DE   AltName: Full=TRM2 homolog B {ECO:0000305};
DE   AltName: Full=rRNA (uracil-5-)-methyltransferase TRMT2B {ECO:0000305};
DE            EC=2.1.1.- {ECO:0000250|UniProtKB:Q96GJ1};
DE   Flags: Precursor;
GN   Name=TRMT2B;
OS   Pongo abelii (Sumatran orangutan) (Pongo pygmaeus abelii).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Pongo.
OX   NCBI_TaxID=9601;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   TISSUE=Kidney;
RG   The German cDNA consortium;
RL   Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases.
CC   -!- FUNCTION: Mitochondrial S-adenosyl-L-methionine-dependent
CC       methyltransferase that catalyzes the formation of 5-methyl-uridine in
CC       tRNAs and 12S rRNA. Catalyzes the methylation of uridine at position 54
CC       (m5U54) in all tRNAs. Specifically methylates the uridine in position
CC       429 of 12S rRNA (m5U429). Does not affect RNA stability or
CC       mitochondrial translation. {ECO:0000250|UniProtKB:Q96GJ1}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=S-adenosyl-L-methionine + uridine(54) in tRNA = 5-
CC         methyluridine(54) in tRNA + H(+) + S-adenosyl-L-homocysteine;
CC         Xref=Rhea:RHEA:42712, Rhea:RHEA-COMP:10167, Rhea:RHEA-COMP:10193,
CC         ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC         ChEBI:CHEBI:65315, ChEBI:CHEBI:74447; EC=2.1.1.35;
CC         Evidence={ECO:0000250|UniProtKB:Q96GJ1};
CC       PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:42713;
CC         Evidence={ECO:0000250|UniProtKB:Q96GJ1};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=a uridine in 12S rRNA + S-adenosyl-L-methionine = a 5-
CC         methyluridine in 12S rRNA + H(+) + S-adenosyl-L-homocysteine;
CC         Xref=Rhea:RHEA:69859, Rhea:RHEA-COMP:17791, Rhea:RHEA-COMP:17792,
CC         ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC         ChEBI:CHEBI:65315, ChEBI:CHEBI:74447;
CC         Evidence={ECO:0000250|UniProtKB:Q96GJ1};
CC       PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:69860;
CC         Evidence={ECO:0000250|UniProtKB:Q96GJ1};
CC   -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000250|UniProtKB:Q96GJ1}.
CC   -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC       superfamily. RNA M5U methyltransferase family. {ECO:0000255|PROSITE-
CC       ProRule:PRU01024}.
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DR   EMBL; CR857127; CAH89430.1; -; mRNA.
DR   RefSeq; NP_001124606.1; NM_001131134.1.
DR   AlphaFoldDB; Q5RFM7; -.
DR   SMR; Q5RFM7; -.
DR   STRING; 9601.ENSPPYP00000023000; -.
DR   GeneID; 100171443; -.
DR   KEGG; pon:100171443; -.
DR   CTD; 79979; -.
DR   eggNOG; KOG2187; Eukaryota.
DR   InParanoid; Q5RFM7; -.
DR   OrthoDB; 248059at2759; -.
DR   Proteomes; UP000001595; Unplaced.
DR   GO; GO:0005739; C:mitochondrion; ISS:UniProtKB.
DR   GO; GO:0070041; F:rRNA (uridine-C5-)-methyltransferase activity; ISS:UniProtKB.
DR   GO; GO:0030697; F:S-adenosylmethionine-dependent tRNA (m5U54) methyltransferase activity; ISS:UniProtKB.
DR   Gene3D; 3.40.50.150; -; 1.
DR   InterPro; IPR029063; SAM-dependent_MTases_sf.
DR   InterPro; IPR045850; TRM2_euk.
DR   InterPro; IPR025823; tRNA_(uracil-5-)_MeTrfase_met.
DR   InterPro; IPR010280; U5_MeTrfase_fam.
DR   PANTHER; PTHR45904; PTHR45904; 1.
DR   Pfam; PF05958; tRNA_U5-meth_tr; 1.
DR   SUPFAM; SSF53335; SSF53335; 1.
DR   PROSITE; PS51687; SAM_MT_RNA_M5U; 1.
PE   2: Evidence at transcript level;
KW   Methyltransferase; Mitochondrion; Reference proteome; rRNA processing;
KW   S-adenosyl-L-methionine; Transferase; Transit peptide; tRNA processing.
FT   TRANSIT         1..?
FT                   /note="Mitochondrion"
FT                   /evidence="ECO:0000255"
FT   CHAIN           ?..486
FT                   /note="tRNA (uracil-5-)-methyltransferase homolog B"
FT                   /id="PRO_0000311934"
FT   ACT_SITE        433
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT   ACT_SITE        479
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000250|UniProtKB:P23003"
FT   BINDING         305
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT   BINDING         355
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT   BINDING         405
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
SQ   SEQUENCE   486 AA;  54550 MW;  BA26E1B2F8DD7A8E CRC64;
     MAGLFFKPGL LPWYARNPPG WSQLFLGTVC KGDFTRVIAT KCQKGQKSQK KPSHLGPLDG
     SWQERLADVV TPLWRLSYEE QLKVKFAAQK KILQRLESYI QMLNGVSVTT AVPKSERLSC
     LLHPIIPSPV INGYRNKSTF SVNRGPDGNP KTVGFYLGTW RDGNMVCVQS NHLKNIPEKH
     SQVAQYYEVF LRQSPLEPCL VFHEGGYWRE LTVRTNSQGH TMAIITFHPQ NLSQEEFHVQ
     KEIVKEFFIR GPGAACDLTS LYFQESTMTR CSHQQSPYQL LFGEPYIFEE LLSLKIRISP
     DAFFQINTAG AEMLYRTVGE LTGVNSDTIL LDICCGTGVI GLSLSQHTSR VLGIELVEQA
     VEDARWTAAF NGITNSEFHT GRAEKILPGL LKSKEDGQSI VAVVNPARAG LHYKVIQAIR
     NFRAIHTLVF VSCKLHGEST RNVIELCCPP DPAKKLLGEP FVLQQVVPVD LFPHTPHCEL
     VLLFTR