ID C5LCT6_PERM5 Unreviewed; 666 AA.
AC C5LCT6;
DT 28-JUL-2009, integrated into UniProtKB/TrEMBL.
DT 28-JUL-2009, sequence version 1.
DT 27-MAR-2024, entry version 56.
DE RecName: Full=tRNA 4-demethylwyosine synthase (AdoMet-dependent) {ECO:0000256|ARBA:ARBA00012821};
DE EC=4.1.3.44 {ECO:0000256|ARBA:ARBA00012821};
GN ORFNames=Pmar_PMAR011816 {ECO:0000313|EMBL:EER05769.1};
OS Perkinsus marinus (strain ATCC 50983 / TXsc).
OC Eukaryota; Sar; Alveolata; Perkinsozoa; Perkinsea; Perkinsida; Perkinsidae;
OC Perkinsus.
OX NCBI_TaxID=423536 {ECO:0000313|Proteomes:UP000007800};
RN [1] {ECO:0000313|EMBL:EER05769.1, ECO:0000313|Proteomes:UP000007800}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 50983 / TXsc {ECO:0000313|Proteomes:UP000007800};
RA El-Sayed N., Caler E., Inman J., Amedeo P., Hass B., Wortman J.;
RL Submitted (JUL-2008) 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. {ECO:0000256|ARBA:ARBA00025368}.
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 Evidence={ECO:0000256|ARBA:ARBA00000664};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000256|ARBA:ARBA00001966};
CC -!- PATHWAY: tRNA modification; wybutosine-tRNA(Phe) biosynthesis.
CC {ECO:0000256|ARBA:ARBA00004797}.
CC -!- SIMILARITY: Belongs to the TYW1 family.
CC {ECO:0000256|ARBA:ARBA00010115}.
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DR EMBL; GG680918; EER05769.1; -; Genomic_DNA.
DR RefSeq; XP_002773953.1; XM_002773907.1.
DR AlphaFoldDB; C5LCT6; -.
DR EnsemblProtists; EER05769; EER05769; Pmar_PMAR011816.
DR GeneID; 9042971; -.
DR InParanoid; C5LCT6; -.
DR OMA; RNFNMTE; -.
DR OrthoDB; 275822at2759; -.
DR UniPathway; UPA00375; -.
DR Proteomes; UP000007800; Unassembled WGS sequence.
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:InterPro.
DR CDD; cd01335; Radical_SAM; 1.
DR Gene3D; 3.40.50.360; -; 1.
DR Gene3D; 3.20.20.70; Aldolase class I; 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; S-ADENOSYL-L-METHIONINE-DEPENDENT TRNA 4-DEMETHYLWYOSINE SYNTHASE; 1.
DR PANTHER; PTHR13930:SF0; S-ADENOSYL-L-METHIONINE-DEPENDENT TRNA 4-DEMETHYLWYOSINE SYNTHASE TYW1-RELATED; 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 SFLD; SFLDG01071; tRNA_wybutosine-synthesizing; 1.
DR SUPFAM; SSF52218; Flavoproteins; 1.
DR SUPFAM; SSF102114; Radical SAM enzymes; 1.
DR PROSITE; PS50902; FLAVODOXIN_LIKE; 1.
DR PROSITE; PS51918; RADICAL_SAM; 1.
PE 3: Inferred from homology;
KW 4Fe-4S {ECO:0000256|ARBA:ARBA00022485};
KW Iron {ECO:0000256|ARBA:ARBA00023004};
KW Iron-sulfur {ECO:0000256|ARBA:ARBA00023014};
KW Lyase {ECO:0000256|ARBA:ARBA00023239};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723};
KW Plastid {ECO:0000256|ARBA:ARBA00022640};
KW Reference proteome {ECO:0000313|Proteomes:UP000007800};
KW S-adenosyl-L-methionine {ECO:0000256|ARBA:ARBA00022691}.
FT DOMAIN 23..174
FT /note="Flavodoxin-like"
FT /evidence="ECO:0000259|PROSITE:PS50902"
FT DOMAIN 268..512
FT /note="Radical SAM core"
FT /evidence="ECO:0000259|PROSITE:PS51918"
FT REGION 183..220
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 193..212
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 666 AA; 74812 MW; 2A1AA40029527708 CRC64;
MLAAGGFYHA LLSKHYTGPQ RTVKVVYSSR TGTSMKAARR LKAALESSTT RVILLPIDQY
AYEELCEESY LVLLLSTDSE GSPLPNAKSF TEQLKDAVYD FRVDKNLLEK CRVAVIGFGS
EEYPAKYYCK VAKNCDDWLA KLGAQRICPL LCVNDAKEVD KQVGRCIDLI TKAYSRMDKA
SSEAQTADLE DEVGSVASEE STSDTDDDVE DASEGCGSNR KEMVTKKHRA ALTREGYRLV
GSHSAVKLCR WTKHQVRGRG GCYKHSFYGI ESHQCMEATA SLACANKCVF CWRHHRNPVG
RSWTWAQDPP EEIVEGWLGN HSGLIKQLKG VPGVTPERFE EAKRVRHCAL SLVGEPIIYP
QINTALDLLH QNGISTFMVT NGQFPEAIRS LIPVTQLYVS VDASNAKEMK AIDRPLFEDF
WDRFIDSLTA LKHKKQRTVY RMTLVKGYNI SAASEYAELL HLGHPHFLEI KAVTFCGKGD
GSAQMTMENV PWFDEVVEFA EAMLDSSDWV KERYEIACTH RHSCTVLIAQ KSFKVDGVWH
TWINYDKFTE LALEYSKTGK PFSVEDYWAP TPAWAVYGAE EEGFDPEMKR HYRNGKTAEL
GKQIRARQLR EEREKAAECG FGSLAAQGRG LDRSSVDSYF VVISTVVILK VAVEELARVS
NSIVVQ
//
