TYW1_PONAB
ID TYW1_PONAB Reviewed; 732 AA.
AC Q5REF9;
DT 03-APR-2007, integrated into UniProtKB/Swiss-Prot.
DT 21-DEC-2004, sequence version 1.
DT 03-AUG-2022, entry version 82.
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 Pongo abelii (Sumatran orangutan) (Pongo pygmaeus abelii).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Pongo.
OX NCBI_TaxID=9601;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Heart;
RG The German cDNA consortium;
RL Submitted (NOV-2004) 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; CR857570; CAH89848.1; -; mRNA.
DR RefSeq; NP_001124859.1; NM_001131387.1.
DR AlphaFoldDB; Q5REF9; -.
DR SMR; Q5REF9; -.
DR STRING; 9601.ENSPPYP00000019631; -.
DR PRIDE; Q5REF9; -.
DR Ensembl; ENSPPYT00000020403; ENSPPYP00000019631; ENSPPYG00000017514.
DR GeneID; 100171721; -.
DR KEGG; pon:100171721; -.
DR CTD; 55253; -.
DR eggNOG; KOG1160; Eukaryota.
DR GeneTree; ENSGT00510000047059; -.
DR InParanoid; Q5REF9; -.
DR OrthoDB; 731783at2759; -.
DR UniPathway; UPA00375; -.
DR Proteomes; UP000001595; Chromosome 7.
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; 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..732
FT /note="S-adenosyl-L-methionine-dependent tRNA 4-
FT demethylwyosine synthase TYW1"
FT /id="PRO_0000281829"
FT DOMAIN 79..237
FT /note="Flavodoxin-like"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00088"
FT DOMAIN 400..644
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT REGION 248..312
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 256..304
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 416
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255"
FT BINDING 420
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"
SQ SEQUENCE 732 AA; 83712 MW; DD8336D70446AFBB CRC64;
MDPSMDTWDL SSPLISLWIN RFYIYLGFAV SISLWICVQI VIKTQGRNLQ EKSVPKAAQD
LMTNGYVSLQ EKDVFVSGVK IFYGSQTGTA KGFATVLAEA VTSLDLPVAI INLKEYDPDD
HLIEEVTSKN VCVFLVATYT DGLPTESAEW FCKWLEEAAI DFRFGKTYLK GMRYAVFGLG
NSAYASHFNK VGKNVDKWLW MLGAHRVMSR GEGDCDVVKS KHGSIEADFR AWKTKFISQL
QALQKGERKK SCGGHCKKGK CESHQRGSEE REEGSHEQDE LHHRDTEEEE PFESSSEEEF
GGKDHQSLNS IVDVEDLGKI MDHVKKEKRE KEQREEKSGL FRNMGRNEDG EIRAMITPAL
REALTKQGYQ LIGSHSGVKL CRWTKSMLRG RGGCYKHTFY GIESHRCMET TPSLACANKC
VFCWRHHTNP VGTEWRWKMD QPEMILKEAI ENHQNMIKQF KGVPGVKAER FEEGMTVKHC
ALSLVGEPIM YPEINRFLKL LHQCKISSFL VTNAQFPAEI RNLEPVTQLY VSVDASTKDS
LKKIDRPLFK DFWRRFLDSL KALAVKQQRT VYRLTLVKAW NVDELQAYAQ LVSLGNPDFI
EVKGVTYCGE SSASSLTMAH VPWHEEVVQF VCELVDLIPD YEIACEHEHS NCLLIAHKKF
KIGGEWWTWI DYNRFQELIQ EYEDSSGSKT FSAKDYMART PHWALFGANE RGFDPKDTRH
QRKNKSKAIS GC
