TYW1_ARATH
ID TYW1_ARATH Reviewed; 647 AA.
AC Q8RXN5; Q9FRL1;
DT 03-APR-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 1.
DT 03-AUG-2022, entry version 114.
DE RecName: Full=S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase;
DE EC=4.1.3.44;
DE AltName: Full=tRNA wybutosine-synthesizing protein 1 homolog;
GN Name=TYW1; OrderedLocusNames=At1g75200; ORFNames=F22H5.13;
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=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
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: Probable 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. Catalyzes the condensation of N-methylguanine with 2 carbon atoms
CC from pyruvate to form the tricyclic 4-demethylwyosine, an intermediate
CC in wybutosine biosynthesis (By similarity). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=N(1)-methylguanosine(37) in tRNA(Phe) + pyruvate + S-adenosyl-
CC L-methionine = 4-demethylwyosine(37) in tRNA(Phe) + 5'-deoxyadenosine
CC + CO2 + H2O + L-methionine; Xref=Rhea:RHEA:36347, Rhea:RHEA-
CC COMP:10164, Rhea:RHEA-COMP:10165, ChEBI:CHEBI:15361,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:16526, ChEBI:CHEBI:17319,
CC ChEBI:CHEBI:57844, ChEBI:CHEBI:59789, ChEBI:CHEBI:64315,
CC ChEBI:CHEBI:73542; EC=4.1.3.44;
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883; Evidence={ECO:0000250};
CC Note=Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3
CC cysteines and an exchangeable S-adenosyl-L-methionine. {ECO:0000250};
CC -!- PATHWAY: tRNA modification; wybutosine-tRNA(Phe) biosynthesis.
CC -!- SIMILARITY: Belongs to the TYW1 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAG12693.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC025814; AAG12693.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE35687.1; -; Genomic_DNA.
DR EMBL; AY114005; AAM45053.1; -; mRNA.
DR EMBL; AY080784; AAL87267.1; -; mRNA.
DR PIR; C96782; C96782.
DR RefSeq; NP_177656.2; NM_106176.6.
DR AlphaFoldDB; Q8RXN5; -.
DR SMR; Q8RXN5; -.
DR STRING; 3702.AT1G75200.1; -.
DR SwissPalm; Q8RXN5; -.
DR PaxDb; Q8RXN5; -.
DR PRIDE; Q8RXN5; -.
DR ProteomicsDB; 243232; -.
DR EnsemblPlants; AT1G75200.1; AT1G75200.1; AT1G75200.
DR GeneID; 843857; -.
DR Gramene; AT1G75200.1; AT1G75200.1; AT1G75200.
DR KEGG; ath:AT1G75200; -.
DR Araport; AT1G75200; -.
DR TAIR; locus:2025152; AT1G75200.
DR eggNOG; KOG1160; Eukaryota.
DR HOGENOM; CLU_007952_2_0_1; -.
DR InParanoid; Q8RXN5; -.
DR OMA; WMLGARR; -.
DR OrthoDB; 731783at2759; -.
DR PhylomeDB; Q8RXN5; -.
DR UniPathway; UPA00375; -.
DR PRO; PR:Q8RXN5; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q8RXN5; baseline and differential.
DR Genevisible; Q8RXN5; AT.
DR GO; GO:0005739; C:mitochondrion; HDA:TAIR.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0010181; F:FMN binding; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0016651; F:oxidoreductase activity, acting on NAD(P)H; IEA:UniProt.
DR GO; GO:0102521; F:tRNA-4-demethylwyosine synthase activity; IEA:UniProtKB-EC.
DR GO; GO:0031591; P:wybutosine biosynthetic process; IBA:GO_Central.
DR Gene3D; 3.20.20.70; -; 1.
DR Gene3D; 3.40.50.360; -; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR001094; Flavdoxin-like.
DR InterPro; IPR008254; Flavodoxin/NO_synth.
DR InterPro; IPR029039; Flavoprotein-like_sf.
DR InterPro; IPR007197; rSAM.
DR InterPro; IPR013917; tRNA_wybutosine-synth.
DR InterPro; IPR034556; tRNA_wybutosine-synthase.
DR PANTHER; PTHR13930; PTHR13930; 1.
DR Pfam; PF00258; Flavodoxin_1; 1.
DR Pfam; PF04055; Radical_SAM; 1.
DR Pfam; PF08608; Wyosine_form; 1.
DR PRINTS; PR00369; FLAVODOXIN.
DR SFLD; SFLDF00284; tRNA_wybutosine-synthesizing; 1.
DR SUPFAM; SSF52218; SSF52218; 1.
DR PROSITE; PS50902; FLAVODOXIN_LIKE; 1.
DR PROSITE; PS51918; RADICAL_SAM; 1.
PE 2: Evidence at transcript level;
KW 4Fe-4S; Iron; Iron-sulfur; Lyase; Metal-binding; Nucleotide-binding;
KW Reference proteome; S-adenosyl-L-methionine; tRNA processing.
FT CHAIN 1..647
FT /note="S-adenosyl-L-methionine-dependent tRNA 4-
FT demethylwyosine synthase"
FT /id="PRO_0000281832"
FT DOMAIN 50..198
FT /note="Flavodoxin-like"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00088"
FT DOMAIN 316..559
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT BINDING 56..60
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00088"
FT BINDING 142..174
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00088"
FT BINDING 332
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT BINDING 336
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255"
FT BINDING 339
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255"
SQ SEQUENCE 647 AA; 72080 MW; 406170439AAA6A8F CRC64;
MSTTSSVRVR LAFVALLSAT TFYCIHKYRR LKHLKNLSLN PSSTLKASRG KIFFISQTGT
AKALAQRLHE LCASNDIAFD IVDPHSYEPE DLPKETLVLF IASTWDGGKP PKNGEFLVNW
LGESAEDFRV GSLLLSDCKF AVFGVGSRAY GESYNAVAKE LSSRMIGLGG LEMIPVGEGD
VDDGELDRAF QDWCDGVIRV LKGGSAQETN GVSQQIGAVE DDLEYYDSTD EEDEDNDADG
GIVDLEDIAG KAPSKRNGVV KVTKVDGKKE MVTPVIRASL TKQGYKIIGS HSGVKICRWT
KSQLRGRGGC YKHSFYGIES HRCMETTPSL ACANKCVFCW RHHTNPVGKS WQWKMDEPSV
IVKGALDLHK NMIKQMKGVP GVTPEKLQEG LNPRHCALSL VGEPIMYPEI NALVDELHGR
RISTFLVTNA QFPEKILMMK PITQLYVSVD AATKESLKAI DRPLFADFWE RFIDSLKALQ
EKQQRTVYRL TLVKGWNTEE LDAYFNLFSI GKPDFIEIKG VTYCGSSATS KLTMENVPWH
TDVKAFSEAL SLKSNGEYEV ACEHAHSCCV LLGRTEKFKV DGKWFTWIDY EKFHDLVASG
EPFTSTDYMA QTPSWAVYGA QEGGFDPGQL RYKKERNHPP KPQAVLA
