TYW4_MOUSE
ID TYW4_MOUSE Reviewed; 686 AA.
AC Q8BYR1; A2ART9; Q3T9F7; Q6A048; Q8BIG6;
DT 24-MAY-2004, integrated into UniProtKB/Swiss-Prot.
DT 27-JUL-2011, sequence version 4.
DT 03-AUG-2022, entry version 134.
DE RecName: Full=tRNA wybutosine-synthesizing protein 4;
DE Short=tRNA yW-synthesizing protein 4;
DE EC=2.1.1.290;
DE EC=2.3.1.231;
DE AltName: Full=Leucine carboxyl methyltransferase 2;
DE AltName: Full=p21WAF1/CIP1 promoter-interacting protein;
DE AltName: Full=tRNA(Phe) (7-(3-amino-3-(methoxycarbonyl)propyl)wyosine(37)-N)-methoxycarbonyltransferase;
DE AltName: Full=tRNA(Phe) (7-(3-amino-3-carboxypropyl)wyosine(37)-O)-methyltransferase;
GN Name=Lcmt2; Synonyms=Kiaa0547, Tyw4;
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Fetal brain;
RX PubMed=15368895; DOI=10.1093/dnares/11.3.205;
RA Okazaki N., Kikuno R., Ohara R., Inamoto S., Koseki H., Hiraoka S.,
RA Saga Y., Seino S., Nishimura M., Kaisho T., Hoshino K., Kitamura H.,
RA Nagase T., Ohara O., Koga H.;
RT "Prediction of the coding sequences of mouse homologues of KIAA gene: IV.
RT The complete nucleotide sequences of 500 mouse KIAA-homologous cDNAs
RT identified by screening of terminal sequences of cDNA clones randomly
RT sampled from size-fractionated libraries.";
RL DNA Res. 11:205-218(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=C57BL/6J;
RX PubMed=19468303; DOI=10.1371/journal.pbio.1000112;
RA Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X.,
RA Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y.,
RA Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S.,
RA Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R.,
RA Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K.,
RA Eichler E.E., Ponting C.P.;
RT "Lineage-specific biology revealed by a finished genome assembly of the
RT mouse.";
RL PLoS Biol. 7:E1000112-E1000112(2009).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 72-686 (ISOFORMS 1 AND 2).
RC STRAIN=C57BL/6J; TISSUE=Hypothalamus, Ovary, and Spleen;
RX PubMed=16141072; DOI=10.1126/science.1112014;
RA Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT "The transcriptional landscape of the mammalian genome.";
RL Science 309:1559-1563(2005).
CC -!- FUNCTION: Probable S-adenosyl-L-methionine-dependent methyltransferase
CC that acts as a component of the wybutosine biosynthesis pathway.
CC Wybutosine is a hyper modified guanosine with a tricyclic base found at
CC the 3'-position adjacent to the anticodon of eukaryotic phenylalanine
CC tRNA (By similarity). May methylate the carboxyl group of leucine
CC residues to form alpha-leucine ester residues. {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=7-[(3S)-3-amino-3-carboxypropyl]wyosine(37) in tRNA(Phe) + S-
CC adenosyl-L-methionine = 7-[(3S)-(3-amino-3-
CC methoxycarbonyl)propyl]wyosine(37) in tRNA(Phe) + S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:36903, Rhea:RHEA-COMP:10379, Rhea:RHEA-
CC COMP:11844, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:73543,
CC ChEBI:CHEBI:74275; EC=2.1.1.290;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=7-[(3S)-(3-amino-3-methoxycarbonyl)propyl]wyosine(37) in
CC tRNA(Phe) + CO2 + S-adenosyl-L-methionine = 2 H(+) + S-adenosyl-L-
CC homocysteine + wybutosine(37) in tRNA(Phe); Xref=Rhea:RHEA:37119,
CC Rhea:RHEA-COMP:11844, Rhea:RHEA-COMP:11847, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16526, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:73544, ChEBI:CHEBI:74275; EC=2.3.1.231;
CC -!- PATHWAY: tRNA modification; wybutosine-tRNA(Phe) biosynthesis.
CC -!- SUBUNIT: Interacts with RNF144B/IBRDC2. {ECO:0000250}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q8BYR1-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8BYR1-2; Sequence=VSP_010357, VSP_010358;
CC -!- SIMILARITY: Belongs to the methyltransferase superfamily. LCMT family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAC35760.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=BAD32248.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AK172970; BAD32248.1; ALT_INIT; mRNA.
DR EMBL; AL845479; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AK038626; BAC30070.1; -; mRNA.
DR EMBL; AK054392; BAC35760.1; ALT_INIT; mRNA.
DR EMBL; AK172552; BAE43064.1; -; mRNA.
DR CCDS; CCDS50682.1; -. [Q8BYR1-1]
DR RefSeq; NP_808514.2; NM_177846.3. [Q8BYR1-1]
DR AlphaFoldDB; Q8BYR1; -.
DR SMR; Q8BYR1; -.
DR BioGRID; 236779; 2.
DR STRING; 10090.ENSMUSP00000106302; -.
DR iPTMnet; Q8BYR1; -.
DR PhosphoSitePlus; Q8BYR1; -.
DR EPD; Q8BYR1; -.
DR MaxQB; Q8BYR1; -.
DR PaxDb; Q8BYR1; -.
DR PRIDE; Q8BYR1; -.
DR ProteomicsDB; 298080; -. [Q8BYR1-1]
DR ProteomicsDB; 298081; -. [Q8BYR1-2]
DR Antibodypedia; 11180; 105 antibodies from 23 providers.
DR Ensembl; ENSMUST00000110674; ENSMUSP00000106302; ENSMUSG00000074890. [Q8BYR1-1]
DR GeneID; 329504; -.
DR KEGG; mmu:329504; -.
DR UCSC; uc008lxn.2; mouse. [Q8BYR1-1]
DR CTD; 9836; -.
DR MGI; MGI:1353659; Lcmt2.
DR VEuPathDB; HostDB:ENSMUSG00000074890; -.
DR eggNOG; KOG2918; Eukaryota.
DR GeneTree; ENSGT00940000162599; -.
DR HOGENOM; CLU_002761_2_0_1; -.
DR InParanoid; Q8BYR1; -.
DR OMA; WEVDFPD; -.
DR OrthoDB; 1094856at2759; -.
DR PhylomeDB; Q8BYR1; -.
DR TreeFam; TF315087; -.
DR UniPathway; UPA00375; -.
DR BioGRID-ORCS; 329504; 0 hits in 72 CRISPR screens.
DR PRO; PR:Q8BYR1; -.
DR Proteomes; UP000000589; Chromosome 2.
DR RNAct; Q8BYR1; protein.
DR Bgee; ENSMUSG00000074890; Expressed in right kidney and 195 other tissues.
DR ExpressionAtlas; Q8BYR1; baseline and differential.
DR Genevisible; Q8BYR1; MM.
DR GO; GO:0003880; F:protein C-terminal carboxyl O-methyltransferase activity; ISA:MGI.
DR GO; GO:0008175; F:tRNA methyltransferase activity; IBA:GO_Central.
DR GO; GO:0006481; P:C-terminal protein methylation; ISA:MGI.
DR GO; GO:0030488; P:tRNA methylation; IBA:GO_Central.
DR GO; GO:0031591; P:wybutosine biosynthetic process; IBA:GO_Central.
DR Gene3D; 2.120.10.80; -; 1.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR015915; Kelch-typ_b-propeller.
DR InterPro; IPR007213; Ppm1/Ppm2/Tcmp.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR Pfam; PF04072; LCM; 1.
DR SUPFAM; SSF117281; SSF117281; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; Methyltransferase; Reference proteome;
KW S-adenosyl-L-methionine; Transferase; tRNA processing.
FT CHAIN 1..686
FT /note="tRNA wybutosine-synthesizing protein 4"
FT /id="PRO_0000204424"
FT REGION 1..23
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 9..23
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 59
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 89
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 114
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 161..162
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 188
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT VAR_SEQ 660..661
FT /note="GG -> QK (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:16141072"
FT /id="VSP_010357"
FT VAR_SEQ 662..686
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:16141072"
FT /id="VSP_010358"
FT CONFLICT 124
FT /note="E -> K (in Ref. 1; BAD32248 and 3; BAE43064)"
FT /evidence="ECO:0000305"
FT CONFLICT 173
FT /note="D -> H (in Ref. 1; BAD32248 and 3; BAE43064)"
FT /evidence="ECO:0000305"
FT CONFLICT 200
FT /note="T -> K (in Ref. 3; BAE43064)"
FT /evidence="ECO:0000305"
FT CONFLICT 250
FT /note="V -> D (in Ref. 1; BAD32248 and 3; BAE43064)"
FT /evidence="ECO:0000305"
FT CONFLICT 558
FT /note="L -> P (in Ref. 1; BAD32248 and 3; BAE43064)"
FT /evidence="ECO:0000305"
FT CONFLICT 655
FT /note="L -> V (in Ref. 3; BAC35760)"
FT /evidence="ECO:0000305"
FT CONFLICT 683
FT /note="R -> C (in Ref. 1; BAD32248 and 3; BAE43064)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 686 AA; 75295 MW; 910183839BCF984C CRC64;
MGPRGRQRRA GTVQSTNDSS SLSKRSLAAH GYVRDPFAAL LVPGPVRRTP LIHRGYYVRA
RAVRHCVRAF LELTSALPSR TRAQILSLGS GSDSLYFRLK AAGLLARAAV WEVDFPDVSR
LKAERIEETP ELRAQTGPFK IGDSASSLCF ESADYRILGA DLRELQRLGE ALDGAGLDAT
SPTLLLAEAV LTYLEPSSAT ALIAWAAQRF PDALFVIYEQ MQPGDAFGQI MLQHFQRLHS
PLHGLELFPV VKAQRQRFLQ AGWTACSALD LNEFYRRLLS AEERQRVETL EPFDEYEEWH
LKCSHYFILA ASRGDILSET PVFEPSEASF QIDPASPSGF LSARVVTSDH QHSSLKRYGH
ASALLSPGVI FSAGGFGEQE GRHCRVSRFH VLSRSCDSEW EGCQISTLGT EGQWDGRLYH
TMTRLSDTRV LVLGGRLSPV SPASGALQLD LYKSKDNCSE GQNVTVTKAA LEEGSVLSCW
RHSTTEVYYQ NQRYLFVYGG RSVAEPVLSD CRFLHVETMA WVRIPVQGAS PEGRHSHSAC
SWQGGALIAG GLGASEELLS SVLFLKPVSS GFLWESIDIQ PSITPRYSHT AHVFNGKLLL
VGGVWIHSSS VPGVTVICLT TGLSSEYQID TASVPWPLML HNHSSALLPE EQQLLLIGGG
GNCFSFGTYF NPHTVALDLS SLRSGQ
