TYW1_DANRE
ID TYW1_DANRE Reviewed; 730 AA.
AC Q08C92;
DT 03-APR-2007, integrated into UniProtKB/Swiss-Prot.
DT 31-OCT-2006, sequence version 1.
DT 03-AUG-2022, entry version 85.
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; ORFNames=zgc:153368;
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Ovary;
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (SEP-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; BC124331; AAI24332.1; -; mRNA.
DR RefSeq; NP_001070624.1; NM_001077156.1.
DR AlphaFoldDB; Q08C92; -.
DR SMR; Q08C92; -.
DR STRING; 7955.ENSDARP00000117225; -.
DR PaxDb; Q08C92; -.
DR PeptideAtlas; Q08C92; -.
DR PRIDE; Q08C92; -.
DR GeneID; 562076; -.
DR KEGG; dre:562076; -.
DR CTD; 55253; -.
DR ZFIN; ZDB-GENE-060929-688; tyw1.
DR eggNOG; KOG1160; Eukaryota.
DR InParanoid; Q08C92; -.
DR OrthoDB; 731783at2759; -.
DR PhylomeDB; Q08C92; -.
DR UniPathway; UPA00375; -.
DR PRO; PR:Q08C92; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Unplaced.
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 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..730
FT /note="S-adenosyl-L-methionine-dependent tRNA 4-
FT demethylwyosine synthase TYW1"
FT /id="PRO_0000281830"
FT DOMAIN 79..237
FT /note="Flavodoxin-like"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00088"
FT DOMAIN 398..642
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT REGION 253..351
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 264..286
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 314..351
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 85..89
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00088"
FT BINDING 176..208
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00088"
FT BINDING 414
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255"
FT BINDING 418
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255"
FT BINDING 421
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255"
SQ SEQUENCE 730 AA; 83549 MW; 4ADA626B453E5F56 CRC64;
MSGVLNDVRD YTEGYLQVLW QNRLYVYSTA AVLIGVWFTV NMLFKKKKMV HPVSPLASKS
VKKQEPASEA KKVIYVSGVK VFYGSQTGTA KGFAKELAED VIAQGIQCEV IDMKDFDPED
RLAEECTSKI ICVFLVATYT DGQPTESAEW FCKWLEEAST DFRYGKTYLK GMRYAVFGLG
NSVYVGHFNT VSKSIDKWLW MLSAARIMTR GEGDCNVVKS RHGSVQADFQ VWKGKFLNRL
QALAKGEKKA CSGNCKKASC KNKKKHKEEA EDNHSLAEKN NSEEELMESS SDEESSSEDE
KSHGSVIDME DLGNVMNHMK KAKQRMEEDE EDSQRVKQNG ERKSECEEER REMITPALRD
SLTKQGYKLI GSHSGVKLRR WTKSMLRGRG GCYKHTFYGI ESHRCMETTP SLACANKCVF
CWRHHTNPVG TEWRWKMDPA EKIIQEAMEN HRNMIRQFRG VPGVRPERFE EGLTVKHCAL
SLVGEPIMYP EINSFLKLLH QQNISSFLVT NAQFPEEIRS LVPVTQLYVS VDASTKDSLK
KIDRPLFKDF WQRFLDSLRA LGEKQQRTVY RLTLVKAWNV DELKAYADLI ALGQPDFIEV
KGVTYCGESS ASSLTMANVP WHEEVIYFVQ QLANLLPDYE IACEHEHSNC LLLANHKFKV
DGEWWTWIDY ERFQELIQQY EESGGTKNFS AMDYMAKTPS WAVFGAGERG FDPTDTRFQR
KNKTKDISGC
