ID A0A1S3UBM4_VIGRR Unreviewed; 1377 AA.
AC A0A1S3UBM4;
DT 12-APR-2017, integrated into UniProtKB/TrEMBL.
DT 12-APR-2017, sequence version 1.
DT 27-MAR-2024, entry version 31.
DE RecName: Full=tRNA 4-demethylwyosine synthase (AdoMet-dependent) {ECO:0000256|ARBA:ARBA00012821};
DE EC=4.1.3.44 {ECO:0000256|ARBA:ARBA00012821};
GN Name=LOC106763782 {ECO:0000313|RefSeq:XP_014503425.1};
OS Vigna radiata var. radiata (Mung bean) (Phaseolus aureus).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade;
OC NPAAA clade; indigoferoid/millettioid clade; Phaseoleae; Vigna.
OX NCBI_TaxID=3916 {ECO:0000313|Proteomes:UP000087766, ECO:0000313|RefSeq:XP_014503425.1};
RN [1] {ECO:0000313|RefSeq:XP_014503425.1}
RP IDENTIFICATION.
RC TISSUE=Leaf {ECO:0000313|RefSeq:XP_014503425.1};
RG RefSeq;
RL Submitted (NOV-2023) to UniProtKB.
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}.
CC -!- SIMILARITY: Belongs to the methyltransferase superfamily.
CC {ECO:0000256|ARBA:ARBA00008361}.
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DR RefSeq; XP_014503425.1; XM_014647939.2.
DR STRING; 3916.A0A1S3UBM4; -.
DR GeneID; 106763782; -.
DR KEGG; vra:106763782; -.
DR OrthoDB; 1202783at2759; -.
DR UniPathway; UPA00375; -.
DR Proteomes; UP000087766; Chromosome 6.
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:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0008168; F:methyltransferase activity; IEA:UniProtKB-KW.
DR GO; GO:0102521; F:tRNA-4-demethylwyosine synthase activity; IEA:UniProtKB-EC.
DR GO; GO:0032259; P:methylation; IEA:UniProtKB-KW.
DR GO; GO:0008033; P:tRNA processing; IEA:InterPro.
DR CDD; cd02440; AdoMet_MTases; 1.
DR CDD; cd01335; Radical_SAM; 1.
DR Gene3D; 3.40.50.360; -; 1.
DR Gene3D; 3.20.20.70; Aldolase class I; 1.
DR Gene3D; 3.40.50.150; Vaccinia Virus protein VP39; 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; IPR004159; Put_SAM_MeTrfase.
DR InterPro; IPR007197; rSAM.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
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; PF03141; Methyltransf_29; 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 SUPFAM; SSF53335; S-adenosyl-L-methionine-dependent methyltransferases; 2.
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 Methyltransferase {ECO:0000256|ARBA:ARBA00022603,
KW ECO:0000313|RefSeq:XP_014503425.1};
KW Reference proteome {ECO:0000313|Proteomes:UP000087766};
KW S-adenosyl-L-methionine {ECO:0000256|ARBA:ARBA00022691};
KW Transferase {ECO:0000256|ARBA:ARBA00022603,
KW ECO:0000313|RefSeq:XP_014503425.1};
KW Transmembrane {ECO:0000256|SAM:Phobius};
KW Transmembrane helix {ECO:0000256|SAM:Phobius}.
FT TRANSMEM 16..37
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT DOMAIN 783..931
FT /note="Flavodoxin-like"
FT /evidence="ECO:0000259|PROSITE:PS50902"
FT DOMAIN 1047..1290
FT /note="Radical SAM core"
FT /evidence="ECO:0000259|PROSITE:PS51918"
FT REGION 48..188
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1355..1377
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 48..64
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 65..82
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 97..154
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 155..173
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 174..188
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 1377 AA; 154457 MW; 1A761BD6E04D3380 CRC64;
MAIARLVRQA KRPHGLWVKM AAVTVMGLCF IFVWGVFSSS SSSVTSQRES FEDIAEPVSS
SSSHKPQKLR DESKKGGESE KKSKSNGNGS SHSSATRPHS EQHKGKDNKK EKKHVQHKED
KEKGNHQGSE EPQPQHGQEE KEKENVKEEV EGEEEKVDHE SDVDVDVDAD GGSDLSESVD
KDDSKVVEDA EELRKKSKVK VKGPLFDPNA SYSWKLCSSR SKHNYIPCID IEVGGGKVTS
YRHTERSCPR TPLMCLVPLP HEGYGSPLPW PESKLKILYK NVAHPKLAAY IKRHNWLMES
EEYLTFPQNQ SEFKGGIHHY LESIEEMVPD IEWGKNIRVV LDIGCTDSSF AAALLDKDVL
TLSLGLKNDL VDLAQVALER GFPAVISPFN RRRLPFPSQV FDAIHCAGCS IPWHSNGGKL
LLEMNRILRP GGYFIMSTKH DSIEEEEAMT TLTASICWNV LAHKSDDVGE VGVKIYQKPE
GNDIYELRRK KIPPLCKENE NPDAVWYVPM KTCLHPIPSG IEQHGAEWPE EWPKRLETYP
DWVNNKEKVV ADTNHWNAVV NKSYISGLGI NWTSIRNVMD MKSIYGGLAV ALSQQKVWVM
NVVPVHAPDT LPIIFERGLV GMYHDWCESF GTYPRTYDLL HADHLFSRLK NRCKQPVSIV
VEMDRITRPG GWTIIRDKVE ILNPLEEILK SMQWEIRMTF AQDKEGILCA QKTFWRPIPL
LHIFSHKSSF STATMSISNS LSSVPARLTL LALFSATTFY CLYKSRRLRY LKLSLNPNPK
PKPKIIFLSE TGTSKTLALR LHRLLASNGV AFDVVDSRHY EPEDLPKETL LXLVASTWQD
GAPPDASRFF ATWLAEASAD FRAGSLLLSS CRVAVFGVGS RAYGESFNAV AKGLATHLRA
LGAKEVVPLC EGDVDGGDLD KVFDRWCEKV LAVLKGGGVX ECDDGDGGGA LDYGVYSSSE
EESDVESEIV DLEDIAGKAP SRRKTLASGE ESNGKLSGRK EMVTPVIRAN LVKQGYKIIG
SHSGVKICRW TKAQLRGRGG CYKHSFYGIE SHRCMEATPS LACANKCVFC WRHHTNPVGK
SWQWEMDDPV EIVNSAVDLH TNMVKQMKGV PGVTLERLNE GLSPRHCALS LVGEPIMYPE
INALVDELHK RRISTFLVTN AQFPEKIKSL KPITQLYVSV DAATKDSLKA IDRPLFGDFW
ERFIDSLTAL REKHQRTVYR LTLVKGWNTE DVDAYSKLFS IGDPDFVEIK GVTYCGTSTT
SKITMENVPW HADVKAFSEA LALKSQGEYE VACEHAHSCC VLLAKTNKFK IDGRWYTWID
YEKFHDLVAS GKTFDSRDYM TATPSWAIYG SKEGGFDPGQ LRYKKERHHK SSHNQSG
//
