TYW1_XENLA
ID TYW1_XENLA Reviewed; 735 AA.
AC Q2KHP8;
DT 03-APR-2007, integrated into UniProtKB/Swiss-Prot.
DT 07-MAR-2006, sequence version 1.
DT 03-AUG-2022, entry version 69.
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 Xenopus laevis (African clawed frog).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia;
OC Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Xenopus.
OX NCBI_TaxID=8355;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Brain;
RG NIH - Xenopus Gene Collection (XGC) project;
RL Submitted (FEB-2006) to the EMBL/GenBank/DDBJ databases.
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}.
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DR EMBL; BC112954; AAI12955.1; -; mRNA.
DR RefSeq; NP_001089965.1; NM_001096496.1.
DR AlphaFoldDB; Q2KHP8; -.
DR SMR; Q2KHP8; -.
DR DNASU; 735035; -.
DR GeneID; 735035; -.
DR KEGG; xla:735035; -.
DR CTD; 735035; -.
DR Xenbase; XB-GENE-5955864; tyw1.S.
DR OrthoDB; 731783at2759; -.
DR UniPathway; UPA00375; -.
DR Proteomes; UP000186698; Chromosome 2S.
DR Bgee; 735035; Expressed in egg cell and 19 other tissues.
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:0008033; P:tRNA processing; IEA:UniProtKB-KW.
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..735
FT /note="S-adenosyl-L-methionine-dependent tRNA 4-
FT demethylwyosine synthase TYW1"
FT /id="PRO_0000281831"
FT DOMAIN 83..241
FT /note="Flavodoxin-like"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00088"
FT DOMAIN 403..649
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT REGION 253..356
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 275..300
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 322..356
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 89..93
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00088"
FT BINDING 180..212
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00088"
FT BINDING 419
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255"
FT BINDING 423
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255"
FT BINDING 426
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255"
SQ SEQUENCE 735 AA; 84114 MW; F75384A3F59EC415 CRC64;
MDKSTDAWDF AYTHLMFLWL NRFYIYSCAA IGITVWVCSH FIMARKKHQN ETVCNGSLLL
KTKALKSDSL TSNKEQKVYV AGVKIFYGSQ TGTSKGFAHL LAEEVTLLGL PVELINMKEY
DPDDNLVEET TSKNICVFLV ATYTDGKPPE SAEWFCKWLE EASNDFRFGK TYLKGMRYAV
FGLGNSVYST HYNTVGKNID KWLWMLSANR VMTRAEGDCN VVKSKHGSIE SDFEAWKRKF
LNRLKALLSG EKKPCSGKCK KGKCKSKKKS SIESVEEEEE EEEKHSEHED TEDDTFETSS
DSEPEEHGEP GSGLIDVEDL GKAMSNMKKS KREHDSNTEL GKSLQGDEAK EKEEPREMIT
PALQEALTKQ GYRLIGSHSG VKLCRWTKSM LRGRGGCYKH TFYGIESHRC METTPSLACA
NKCVFCWRHH TNPVGTEWRW KMDQPEMILE EAILNHQNMI KQFKGVPGVK PERFEEGLAV
KHCALSLVGE PIMYPEINTF LRLLHNQHIS SFLVTNAQFP EEIRSLEPVT QLYVSVDAST
KDSLKKIDRP LFKDFWQRFI DSLKALAEKQ QRTVYRLTLV KAWNVDELKA YADLVALGLP
DFIEVKGVTY CGESSASNLT MANVPWHEEV IRFVEELVDL LPDYEVACEH EHSNCMLIAH
KKFKINGEWC TWIDYERFQE LIQAFGESKG SRTFTALDYV AKTPEWALFG SRERGFDPLD
KRFQRKNKTK DISGC
