TYW1_MOUSE
ID TYW1_MOUSE Reviewed; 721 AA.
AC Q8BJM7; Q3TRC5; Q8BLG4; Q8R0C7;
DT 03-APR-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 144.
DE RecName: Full=S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1;
DE EC=4.1.3.44;
DE AltName: Full=Radical S-adenosyl methionine and flavodoxin domain-containing protein 1;
DE AltName: Full=tRNA wybutosine-synthesizing protein 1 homolog;
DE AltName: Full=tRNA-yW-synthesizing protein;
GN Name=Tyw1; Synonyms=Rsafd1;
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] (ISOFORMS 1 AND 2).
RC STRAIN=C57BL/6J; TISSUE=Hypothalamus;
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).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=C57BL/6J, and FVB/N; TISSUE=Brain, and Mammary tumor;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [3]
RP PROTEIN SEQUENCE OF 159-165, AND IDENTIFICATION BY MASS SPECTROMETRY.
RC STRAIN=OF1; TISSUE=Hippocampus;
RA Lubec G., Sunyer B., Chen W.-Q.;
RL Submitted (JAN-2009) to UniProtKB.
RN [4]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Kidney;
RX PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
RA Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
RA Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
RT "A tissue-specific atlas of mouse protein phosphorylation and expression.";
RL Cell 143:1174-1189(2010).
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 -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q8BJM7-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8BJM7-3; Sequence=VSP_024068, VSP_024070;
CC -!- SIMILARITY: Belongs to the TYW1 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAC32293.1; Type=Miscellaneous discrepancy; Note=Probable cloning artifact.; Evidence={ECO:0000305};
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DR EMBL; AK045279; BAC32293.1; ALT_SEQ; mRNA.
DR EMBL; AK082884; BAC38668.1; -; mRNA.
DR EMBL; AK162899; BAE37105.1; -; mRNA.
DR EMBL; BC027065; AAH27065.1; -; mRNA.
DR EMBL; BC068126; AAH68126.1; -; mRNA.
DR CCDS; CCDS19712.1; -. [Q8BJM7-1]
DR RefSeq; NP_001015876.1; NM_001015876.2. [Q8BJM7-1]
DR RefSeq; NP_849228.1; NM_178897.4.
DR RefSeq; XP_006504394.1; XM_006504331.2. [Q8BJM7-1]
DR AlphaFoldDB; Q8BJM7; -.
DR SMR; Q8BJM7; -.
DR BioGRID; 221556; 2.
DR IntAct; Q8BJM7; 1.
DR STRING; 10090.ENSMUSP00000037173; -.
DR iPTMnet; Q8BJM7; -.
DR PhosphoSitePlus; Q8BJM7; -.
DR EPD; Q8BJM7; -.
DR MaxQB; Q8BJM7; -.
DR PaxDb; Q8BJM7; -.
DR PeptideAtlas; Q8BJM7; -.
DR PRIDE; Q8BJM7; -.
DR ProteomicsDB; 297683; -. [Q8BJM7-1]
DR ProteomicsDB; 297684; -. [Q8BJM7-3]
DR DNASU; 100929; -.
DR Ensembl; ENSMUST00000040213; ENSMUSP00000037173; ENSMUSG00000056310. [Q8BJM7-1]
DR Ensembl; ENSMUST00000100662; ENSMUSP00000098226; ENSMUSG00000056310. [Q8BJM7-3]
DR GeneID; 100929; -.
DR KEGG; mmu:100929; -.
DR UCSC; uc008zul.2; mouse. [Q8BJM7-1]
DR CTD; 55253; -.
DR MGI; MGI:2141161; Tyw1.
DR VEuPathDB; HostDB:ENSMUSG00000056310; -.
DR eggNOG; KOG1160; Eukaryota.
DR GeneTree; ENSGT00510000047059; -.
DR HOGENOM; CLU_007952_2_0_1; -.
DR InParanoid; Q8BJM7; -.
DR OMA; WMLGARR; -.
DR OrthoDB; 731783at2759; -.
DR PhylomeDB; Q8BJM7; -.
DR TreeFam; TF300773; -.
DR UniPathway; UPA00375; -.
DR BioGRID-ORCS; 100929; 0 hits in 71 CRISPR screens.
DR ChiTaRS; Tyw1; mouse.
DR PRO; PR:Q8BJM7; -.
DR Proteomes; UP000000589; Chromosome 5.
DR RNAct; Q8BJM7; protein.
DR Bgee; ENSMUSG00000056310; Expressed in ear vesicle and 204 other tissues.
DR ExpressionAtlas; Q8BJM7; baseline and differential.
DR Genevisible; Q8BJM7; MM.
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: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; SFLDS00029; Radical_SAM; 1.
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 1: Evidence at protein level;
KW 4Fe-4S; Alternative splicing; Direct protein sequencing; Iron; Iron-sulfur;
KW Lyase; Metal-binding; Nucleotide-binding; Reference proteome;
KW S-adenosyl-L-methionine; tRNA processing.
FT CHAIN 1..721
FT /note="S-adenosyl-L-methionine-dependent tRNA 4-
FT demethylwyosine synthase TYW1"
FT /id="PRO_0000281828"
FT DOMAIN 71..229
FT /note="Flavodoxin-like"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00088"
FT DOMAIN 389..635
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT REGION 242..291
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 305..339
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 309..339
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 77..81
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00088"
FT BINDING 168..200
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00088"
FT BINDING 405
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255"
FT BINDING 409
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255"
FT BINDING 412
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255"
FT VAR_SEQ 318..386
FT /note="REKSHQDGKAAMQRNPEKTEDGEGRAMITPALREALTKQGYQLIGSHSGVKL
FT CRWTKSMLRGRGGCYKH -> TSCSALSSYSDSAMSHHNKEKSVRPPSLIQRLLQQVLS
FT MTVGWRRRSSEDSQVQGTSSARKWRPGRRPL (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:16141072"
FT /id="VSP_024068"
FT VAR_SEQ 387..721
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:16141072"
FT /id="VSP_024070"
SQ SEQUENCE 721 AA; 81599 MW; EDDC14A91335A8FE CRC64;
MGPLDVWDLS PLLSLWMNRF YIYMGCALGL TLCICVQIIK KQVTRSQEKR VPGAPDSSLS
PQKKQTHVSG VKIFYGSQTG TAKGFAVVLA KAVTSLDLPV AIINLKEYDP DDSLIGEITS
KTVCAFLVAT YTDGCPTESA EWFCKWLEES ANDFRFGKTY LKGLRYAVFG LGDSAYRSHF
NKVSTNVDKW LWMLGAQRVL TRGEGDCNAV QSKHGSIEAD FTAWKTKFIS RLQALQRGEK
KACGGNCKRG KCESAQHGPG EARPHPQGEL HPGDAEEEEP CESSSEDELG TQDYQSLTSV
VDVEDLGNIM NPVKREKREK SHQDGKAAMQ RNPEKTEDGE GRAMITPALR EALTKQGYQL
IGSHSGVKLC RWTKSMLRGR GGCYKHTFYG IESHRCMEAT PSLACANKCV FCWRHHTNPV
GTEWRWKMDQ PELILKEAIE NHQNMIKQFK GVPGLKAERF EEGMEVKHCA LSLVGEPIMY
PEINRLLKLL HQHGISSFLV TNAQFPEEIR KLTPVTQLYV SVDASTRDGL KKIDRPLFKD
FWQRFLDSLK ALSAKQQRTV YRLTLVKCWN VDELQAYAEL VSLGNPDFIE VKGVTYCGES
AASSLTMANV PWHEEVVRFV RELVDLLPDY EVACEHEHSN CLLIGHKKFK IDGEWWTWIN
YSRFQELVLQ YEESGGSKTF SSRDYMARTP QWALFGARER GFDPKDTRYQ RKNKTKDISG
C
