TYW23_ARATH
ID TYW23_ARATH Reviewed; 995 AA.
AC Q8W4K1; Q9S9V3;
DT 03-APR-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 130.
DE RecName: Full=tRNA wybutosine-synthesizing protein 2/3/4;
DE Includes:
DE RecName: Full=tRNA wybutosine-synthesizing protein 3 homolog;
DE Short=tRNA-yW-synthesizing protein 3;
DE EC=2.1.1.282;
DE AltName: Full=tRNA(Phe) 7-((3-amino-3-carboxypropyl)-4-demethylwyosine(37)-N(4))-methyltransferase;
DE Includes:
DE RecName: Full=tRNA wybutosine-synthesizing protein 2 homolog;
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 OrderedLocusNames=At4g04670; ORFNames=T19J18.2;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
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 (By
CC similarity). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=4-demethyl-7-[(3S)-3-amino-3-carboxypropyl]wyosine(37) in
CC tRNA(Phe) + S-adenosyl-L-methionine = 7-[(3S)-3-amino-3-
CC carboxypropyl]wyosine(37) in tRNA(Phe) + H(+) + S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:36635, Rhea:RHEA-COMP:10378, Rhea:RHEA-
CC COMP:10379, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:73543, ChEBI:CHEBI:73550; EC=2.1.1.282;
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 -!- PATHWAY: tRNA modification; wybutosine-tRNA(Phe) biosynthesis.
CC -!- SIMILARITY: In the C-terminal section; belongs to the class I-like SAM-
CC binding methyltransferase superfamily. TRM5/TYW2 family. {ECO:0000305}.
CC -!- SIMILARITY: In the N-terminal section; belongs to the TYW3 family.
CC {ECO:0000305}.
CC -!- CAUTION: In plants, methylation steps 2, 3 and 4 of wybutosine
CC biosynthesis are probably processed by the this multifunctional enzyme,
CC while in other eukaryotes, these steps are mediated by 3 different
CC proteins. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAD48952.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB80832.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AF149414; AAD48952.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161501; CAB80832.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE82410.1; -; Genomic_DNA.
DR EMBL; AY062510; AAL32588.1; -; mRNA.
DR EMBL; BT008367; AAP37726.1; -; mRNA.
DR PIR; H85058; H85058.
DR RefSeq; NP_567268.2; NM_116705.5.
DR AlphaFoldDB; Q8W4K1; -.
DR SMR; Q8W4K1; -.
DR STRING; 3702.AT4G04670.1; -.
DR PaxDb; Q8W4K1; -.
DR PRIDE; Q8W4K1; -.
DR ProteomicsDB; 242603; -.
DR EnsemblPlants; AT4G04670.1; AT4G04670.1; AT4G04670.
DR GeneID; 825800; -.
DR Gramene; AT4G04670.1; AT4G04670.1; AT4G04670.
DR KEGG; ath:AT4G04670; -.
DR Araport; AT4G04670; -.
DR TAIR; locus:2135069; AT4G04670.
DR eggNOG; KOG0379; Eukaryota.
DR eggNOG; KOG1227; Eukaryota.
DR eggNOG; KOG1228; Eukaryota.
DR HOGENOM; CLU_006768_0_0_1; -.
DR InParanoid; Q8W4K1; -.
DR OMA; VIVGIRC; -.
DR OrthoDB; 1263405at2759; -.
DR PhylomeDB; Q8W4K1; -.
DR UniPathway; UPA00375; -.
DR PRO; PR:Q8W4K1; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q8W4K1; baseline and differential.
DR Genevisible; Q8W4K1; AT.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
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; IBA:GO_Central.
DR GO; GO:0031591; P:wybutosine biosynthetic process; ISS:TAIR.
DR Gene3D; 2.120.10.80; -; 2.
DR Gene3D; 3.30.1960.10; -; 1.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR015915; Kelch-typ_b-propeller.
DR InterPro; IPR030382; MeTrfase_TRM5/TYW2.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR InterPro; IPR003827; tRNA_yW-synthesising.
DR InterPro; IPR036602; tRNA_yW-synthesising-like_sf.
DR Pfam; PF02475; Met_10; 1.
DR Pfam; PF02676; TYW3; 1.
DR SUPFAM; SSF111278; SSF111278; 1.
DR SUPFAM; SSF117281; SSF117281; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR PROSITE; PS51684; SAM_MT_TRM5_TYW2; 1.
PE 2: Evidence at transcript level;
KW Kelch repeat; Methyltransferase; Multifunctional enzyme;
KW Reference proteome; Repeat; S-adenosyl-L-methionine; Transferase;
KW tRNA processing.
FT CHAIN 1..995
FT /note="tRNA wybutosine-synthesizing protein 2/3/4"
FT /id="PRO_0000281849"
FT REPEAT 284..335
FT /note="Kelch 1"
FT REPEAT 336..386
FT /note="Kelch 2"
FT REPEAT 387..436
FT /note="Kelch 3"
FT REPEAT 437..486
FT /note="Kelch 4"
FT REPEAT 488..535
FT /note="Kelch 5"
FT REGION 1..212
FT /note="tRNA wybutosine-synthesizing protein 3 homolog"
FT REGION 661..995
FT /note="tRNA wybutosine-synthesizing protein 2 homolog"
FT BINDING 828
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01021"
FT BINDING 896..897
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01021"
SQ SEQUENCE 995 AA; 110856 MW; DCB5824E8762A5B9 CRC64;
MDFEKRKAAT LASIRSSVTD KSPKGFLDEP IIPLLETINH HPSYFTTSSC SGRISILSQP
KPKSNDSTKK KARGGSWLYI THDPADSDLV ISLLFPSKSN QIDPIDQPSE LVFRFEPLII
AVECKDLGSA QFLVALAISA GFRESGITSC GDGKRVIIAI RCSIRMEVPI GDTEKLMVSP
EYVKFLVDIA NEKMDANRKR TDGFSVALAS NGFKNPDEND VDEDDNYENL AANHDSSINN
GNLYPGVQKE LIPLEKLSIV GEPVEKLHLW GHSACTIDES DRKEVIVFGG FGGFGRHARR
NESLLLNPSC GTLKLIAVNE SPSARLGHTA SMVGDFMFVI GGRADPLNIL NDVWRLDIST
GEWSSQRCVG SEFPPRHRHA AASVGTKVYI FGGLYNDKIV SSMHILDTKD LQWKEVEQQG
QWPCARHSHA MVAYGSQSFM FGGYNGENVL NDLYSFDVQS CSWKLEVISG KWPHARFSHS
MFVYKHTIGI IGGCPVSQNC QELTLLDLKH RLWRSVRLEF MNKELFVRST ASILGDDLIV
IGGGAACYAF GTKFSEPVKI NLVQSVTMSE NHLPPQPEDV SLESNKNNAD LKTETSLSQP
WVIQLERKYA KFGKDILKSF GWLDLERKVY SNEKGLCICF PVTENFSELF HEKQLLGKDF
ERSEENNLTK GLSLKDISCS AALNLLKEHG AKKLINVAFE AKKVAKSPLQ RMREDITSIL
KQKGLPEELL DELPQKWERL GDIVVVPATS FKDPTWSSIN DEVWCAVSKS LSANRLARQG
RVEPNGTRDS TLEILVGDNG WVNHRENGIL YSFDATKCMF SWGNLSEKLR MGNMACENEV
VVDLFAGIGY FVLPFLVRAK AKLVYACEWN PHAIEALRRN VEANSVSERC IILEGDNRIT
APKGVADRVN LGLIPSSEGS WVTAIQALRP EGGILHVHGN VKDSDESSWG EHVTKTLSDI
ARAEGRSWEV TVEHIEKVKW YAPRIRHLVA DVRCR
