TYW2_YEAST
ID TYW2_YEAST Reviewed; 462 AA.
AC Q04235; D6VZH0;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 1.
DT 03-AUG-2022, entry version 154.
DE RecName: Full=tRNA wybutosine-synthesizing protein 2;
DE Short=tRNA-yW-synthesizing protein 2;
DE EC=2.5.1.114;
DE AltName: Full=tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase;
GN Name=TRM12; Synonyms=TYW2; OrderedLocusNames=YML005W; ORFNames=YM9571.14;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169872;
RA Bowman S., Churcher C.M., Badcock K., Brown D., Chillingworth T.,
RA Connor R., Dedman K., Devlin K., Gentles S., Hamlin N., Hunt S., Jagels K.,
RA Lye G., Moule S., Odell C., Pearson D., Rajandream M.A., Rice P.,
RA Skelton J., Walsh S.V., Whitehead S., Barrell B.G.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII.";
RL Nature 387:90-93(1997).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [3]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [4]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [5]
RP PATHWAY, AND DISRUPTION PHENOTYPE.
RX PubMed=16005430; DOI=10.1016/j.bbrc.2005.06.111;
RA Kalhor H.R., Penjwini M., Clarke S.;
RT "A novel methyltransferase required for the formation of the hypermodified
RT nucleoside wybutosine in eucaryotic tRNA.";
RL Biochem. Biophys. Res. Commun. 334:433-440(2005).
RN [6]
RP FUNCTION, CATALYTIC ACTIVITY, AND PATHWAY.
RX PubMed=16642040; DOI=10.1038/sj.emboj.7601105;
RA Noma A., Kirino Y., Ikeuchi Y., Suzuki T.;
RT "Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic
RT phenylalanine tRNA.";
RL EMBO J. 25:2142-2154(2006).
RN [7]
RP FUNCTION, AND PATHWAY.
RX PubMed=17150819; DOI=10.1093/nass/nrl032;
RA Noma A., Suzuki T.;
RT "Ribonucleome analysis identified enzyme genes responsible for wybutosine
RT synthesis.";
RL Nucleic Acids Symp. Ser. 50:65-66(2006).
CC -!- FUNCTION: S-adenosyl-L-methionine-dependent transferase that acts as a
CC component of the wybutosine biosynthesis pathway. Wybutosine is a hyper
CC modified guanosine with a tricyclic base found at the 3'-position
CC adjacent to the anticodon of eukaryotic phenylalanine tRNA. Catalyzes
CC the transfer of the alpha-amino-alpha-carboxypropyl (acp) group from S-
CC adenosyl-L-methionine to the C-7 position of 4-demethylwyosine (imG-14)
CC to produce wybutosine-86. {ECO:0000269|PubMed:16642040,
CC ECO:0000269|PubMed:17150819}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=4-demethylwyosine(37) in tRNA(Phe) + S-adenosyl-L-methionine =
CC 4-demethyl-7-[(3S)-3-amino-3-carboxypropyl]wyosine(37) in tRNA(Phe) +
CC H(+) + S-methyl-5'-thioadenosine; Xref=Rhea:RHEA:36355, Rhea:RHEA-
CC COMP:10164, Rhea:RHEA-COMP:10378, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:17509, ChEBI:CHEBI:59789, ChEBI:CHEBI:64315,
CC ChEBI:CHEBI:73550; EC=2.5.1.114;
CC Evidence={ECO:0000269|PubMed:16642040};
CC -!- PATHWAY: tRNA modification; wybutosine-tRNA(Phe) biosynthesis.
CC {ECO:0000269|PubMed:16005430, ECO:0000269|PubMed:16642040,
CC ECO:0000269|PubMed:17150819}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}.
CC -!- DISRUPTION PHENOTYPE: tRNA(Phe) from mutant shows accumulation of 4-
CC demethylwyosine (ImG-14) and absence of wybutosine.
CC {ECO:0000269|PubMed:16005430}.
CC -!- MISCELLANEOUS: Present with 656 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. TRM5/TYW2 family. {ECO:0000255|PROSITE-ProRule:PRU01021}.
CC -!- CAUTION: Was originally thought to be a methyltransferase.
CC {ECO:0000305|PubMed:16005430}.
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DR EMBL; Z49810; CAA89947.1; -; Genomic_DNA.
DR EMBL; BK006946; DAA09894.1; -; Genomic_DNA.
DR PIR; S55114; S55114.
DR RefSeq; NP_013709.1; NM_001182360.1.
DR AlphaFoldDB; Q04235; -.
DR BioGRID; 35166; 77.
DR MINT; Q04235; -.
DR STRING; 4932.YML005W; -.
DR MaxQB; Q04235; -.
DR PaxDb; Q04235; -.
DR PRIDE; Q04235; -.
DR EnsemblFungi; YML005W_mRNA; YML005W; YML005W.
DR GeneID; 855008; -.
DR KEGG; sce:YML005W; -.
DR SGD; S000004464; TRM12.
DR VEuPathDB; FungiDB:YML005W; -.
DR eggNOG; KOG1227; Eukaryota.
DR GeneTree; ENSGT00940000153304; -.
DR HOGENOM; CLU_023588_1_0_1; -.
DR InParanoid; Q04235; -.
DR OMA; AFELNPW; -.
DR BioCyc; MetaCyc:G3O-32610-MON; -.
DR BioCyc; YEAST:G3O-32610-MON; -.
DR BRENDA; 2.5.1.114; 984.
DR UniPathway; UPA00375; -.
DR PRO; PR:Q04235; -.
DR Proteomes; UP000002311; Chromosome XIII.
DR RNAct; Q04235; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0008757; F:S-adenosylmethionine-dependent methyltransferase activity; IDA:SGD.
DR GO; GO:0016765; F:transferase activity, transferring alkyl or aryl (other than methyl) groups; IDA:SGD.
DR GO; GO:0102522; F:tRNA 4-demethylwyosine alpha-amino-alpha-carboxypropyltransferase activity; IEA:UniProtKB-EC.
DR GO; GO:0008175; F:tRNA methyltransferase activity; IBA:GO_Central.
DR GO; GO:0030488; P:tRNA methylation; IDA:SGD.
DR GO; GO:0006400; P:tRNA modification; TAS:Reactome.
DR GO; GO:0031591; P:wybutosine biosynthetic process; IMP:SGD.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR030382; MeTrfase_TRM5/TYW2.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR InterPro; IPR026274; tRNA_wybutosine_synth_prot_2.
DR Pfam; PF02475; Met_10; 1.
DR PIRSF; PIRSF038972; Trm12; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR PROSITE; PS51684; SAM_MT_TRM5_TYW2; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; Reference proteome; S-adenosyl-L-methionine; Transferase;
KW tRNA processing.
FT CHAIN 1..462
FT /note="tRNA wybutosine-synthesizing protein 2"
FT /id="PRO_0000203264"
FT BINDING 257
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01021"
FT BINDING 264
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01021"
FT BINDING 305..306
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01021"
SQ SEQUENCE 462 AA; 52726 MW; C581EF189A7D733C CRC64;
MSDETMPVEF LVSDKRLLKT IKVKLETNGL FVTPIYSDND NKVIKSSIED LNHPLAVEIN
NIAGVKARFH ESGNLERSEG HLKHQSNSIT EFTKSFLKDH GLANDKIFLS HLLDHLPLKY
TIYPPVVLFN NSTVRSFNHP IWQKAFQLKL FDPNEYYREL LCFLSPGKPS KGTSLHPNNR
LLTHLAINNP ITEADVLRRP FNIQPLYGKL IDDSILDDND NTLWENPSQE QLNSSIWCKV
IQNGVTQIWS PVFTMFSRGN IKEKKRVLTT FPDICNNDVV DLYAGIGYFT FSYLTKGART
LFAFELNPWS VEGLKRGLKA NGFNKSGNCH VFQESNEMCV QRLTEFLSQN PGFRLRIRHI
NLGLLPSSKQ GWPLAIKLIY LQGASLEKVT MHIHENVHID AIEDGSFEKN VIVELDAINE
SIALIRNRGI KLQFVRSKLE RIKTFAPDIW HVCVDVDVIV ST
