ID W9RQ06_9ROSA Unreviewed; 778 AA.
AC W9RQ06;
DT 14-MAY-2014, integrated into UniProtKB/TrEMBL.
DT 14-MAY-2014, sequence version 1.
DT 27-MAR-2024, entry version 41.
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=L484_003329 {ECO:0000313|EMBL:EXB63946.1};
OS Morus notabilis.
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; fabids; Rosales; Moraceae; Moreae; Morus.
OX NCBI_TaxID=981085 {ECO:0000313|EMBL:EXB63946.1, ECO:0000313|Proteomes:UP000030645};
RN [1] {ECO:0000313|Proteomes:UP000030645}
RP NUCLEOTIDE SEQUENCE.
RA He N., Zhao S.;
RT "Draft Genome Sequence of a Mulberry Tree, Morus notabilis C.K. Schneid.";
RL Submitted (JAN-2013) 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; KE344493; EXB63946.1; -; Genomic_DNA.
DR RefSeq; XP_010096383.1; XM_010098081.1.
DR AlphaFoldDB; W9RQ06; -.
DR STRING; 981085.W9RQ06; -.
DR eggNOG; KOG1160; Eukaryota.
DR UniPathway; UPA00375; -.
DR Proteomes; UP000030645; Unassembled WGS sequence.
DR GO; GO:0016020; C:membrane; IEA:UniProtKB-KW.
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:0016829; F:lyase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0008033; P:tRNA processing; IEA:InterPro.
DR Gene3D; 3.40.50.360; -; 1.
DR Gene3D; 3.20.20.70; Aldolase class I; 2.
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; SFLDS00029; Radical_SAM; 1.
DR SFLD; SFLDF00284; 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}; Membrane {ECO:0000256|SAM:Phobius};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723};
KW Reference proteome {ECO:0000313|Proteomes:UP000030645};
KW S-adenosyl-L-methionine {ECO:0000256|ARBA:ARBA00022691};
KW Transmembrane {ECO:0000256|SAM:Phobius};
KW Transmembrane helix {ECO:0000256|SAM:Phobius}.
FT TRANSMEM 16..35
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT DOMAIN 62..210
FT /note="Flavodoxin-like"
FT /evidence="ECO:0000259|PROSITE:PS50902"
FT DOMAIN 326..620
FT /note="Radical SAM core"
FT /evidence="ECO:0000259|PROSITE:PS51918"
FT REGION 259..280
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 265..279
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 778 AA; 87034 MW; E71CFE8E365D2756 CRC64;
MAKPEKLLPA MCISSVPARL TLLALLSATT FYCFYKFHRL RSLRISLNPN PNSKSSSCFR
RGKLLFISET GTSKTLARRL LDLLNSNDLA FDLVDAKAYE PEDLPKETQV LIVASTWEDG
KAPPSGRFFA NWLAESVEDF RVGSLLLSQC KFAVFGVGSR AYGATYNVVA RDLSKRMRGL
GAAEMLPVWE GDVDGGDLEE AFDAWSAKMV KVLNDDVVEN GGALSNGVGA ESDAESDYET
DEEYSVESEI VDLEDIAGKG PSRRSPVVVQ TNGTSNGKKD MVTPVIRASL EKQGYKIIGS
HSGVKVCRWT KSQLRGRGGC YKHSFYGIES HRCMEATPSL ACANKCVFCW RHHTNPVGKS
WQWKMDDPLE IVNSAIDQHT KMIKQMKGVP GSHFGRGDLE RPEWAIQSGL LWTSVSEAWW
YLGSWLSPTL LKYGLSISSC AGVTLERLTE GLSPRHCALS LVGEPIMYPE INTLVDELHR
RRISTFLVTN AQFPEKIKML KPITQLYVSV DAATKDSLKA IDRPLFGDFW ERFLDSLKAL
RDKQQRTVYR LTLVKGWNTE DVDAYFNLFS IGKPDFIEIK GVTYCGSSAT SKLTMENVPW
HSEVKAFSEA LALKSQGEYE VACEHVHSCC VLLAKTEKFK INGQWFTWIE YEKFHDLVAS
GKAFDSKDYM AATPSWAVYG AEEGGFDPDQ SRYKKERHHN RPNRATARPV FTLFLIKKCV
FPSSTCSKFY KRELLYPSSI AFSAQLKSGY NKLPIGTGVR AAWVPLKESV NSRIALDK
//
