ID A0A091V1E7_NIPNI Unreviewed; 668 AA.
AC A0A091V1E7;
DT 26-NOV-2014, integrated into UniProtKB/TrEMBL.
DT 26-NOV-2014, sequence version 1.
DT 24-JAN-2024, entry version 32.
DE RecName: Full=tRNA 4-demethylwyosine synthase (AdoMet-dependent) {ECO:0000256|ARBA:ARBA00012821};
DE EC=4.1.3.44 {ECO:0000256|ARBA:ARBA00012821};
DE Flags: Fragment;
GN ORFNames=Y956_15263 {ECO:0000313|EMBL:KFQ96741.1};
OS Nipponia nippon (Crested ibis) (Ibis nippon).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda;
OC Coelurosauria; Aves; Neognathae; Pelecaniformes; Threskiornithidae;
OC Nipponia.
OX NCBI_TaxID=128390 {ECO:0000313|EMBL:KFQ96741.1, ECO:0000313|Proteomes:UP000053283};
RN [1] {ECO:0000313|EMBL:KFQ96741.1, ECO:0000313|Proteomes:UP000053283}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=BGI_Y956 {ECO:0000313|EMBL:KFQ96741.1};
RA Zhang G., Li C.;
RT "Genome evolution of avian class.";
RL Submitted (APR-2014) 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; KL410453; KFQ96741.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A091V1E7; -.
DR STRING; 128390.A0A091V1E7; -.
DR eggNOG; KOG1160; Eukaryota.
DR UniPathway; UPA00375; -.
DR Proteomes; UP000053283; 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: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; 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:UP000053283};
KW S-adenosyl-L-methionine {ECO:0000256|ARBA:ARBA00022691};
KW Transmembrane {ECO:0000256|SAM:Phobius};
KW Transmembrane helix {ECO:0000256|SAM:Phobius}.
FT TRANSMEM 23..42
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT DOMAIN 84..242
FT /note="Flavodoxin-like"
FT /evidence="ECO:0000259|PROSITE:PS50902"
FT DOMAIN 406..650
FT /note="Radical SAM core"
FT /evidence="ECO:0000259|PROSITE:PS51918"
FT REGION 253..318
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 331..358
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 254..287
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 288..306
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT NON_TER 1
FT /evidence="ECO:0000313|EMBL:KFQ96741.1"
FT NON_TER 668
FT /evidence="ECO:0000313|EMBL:KFQ96741.1"
SQ SEQUENCE 668 AA; 75525 MW; 15092FA1A7031794 CRC64;
LDVSMDIWNC CYTCIVSLWL RRFYIYCAVA FGISIWIIIW FTTTKTKKKG EKSNGKPPPS
EGIEDKLLNT SATLQAKEVY VAGVKIFYGS QTGTAKRFAE GLAKAVISLN LPVEVVGMGD
YDPDDCLAEE TTSKNVCVFL VATYTDGQPT ESAAWFCKWL EEAANDFRFG KTYLKGLRYA
VFGLGDSVYV DHYNTVGRNI DRWLWMLSAS RIMTRAEGDC NVAQSKHGSI EADFEAWKAK
FLSRLQALCR GEKKPCSGKC KKGKCKSPEK QSKESSDHER EASEYENTEA EELFETSSEE
EVVDAEEAGG TNSVIDVEDL GNIMSHMKKA KREHELEEGG VGTSLTQEST GRKEEGGKRE
MITPALREAL TKQGYKLIGS HSGVKLCRWT KSMLRGRGGC YKHTFYGIES HRCMEATPSL
ACANKCVFCW RHHTNPVGTE WRWKMDQPER ILQEAIENHQ NMIKQFKGVS GVKADRFEEA
MTAKHCALSL VGEPIMYPEI NRFVKLLHQC SISSFLVTNA QFPDEIRNLE PVTQLYVSVD
ASTKESLKRI DRPLFKDFWQ RFLDSLKALS EKQQRTVYRL TLVKAWNVDE LKAYADLISL
GKPDFIEVKG VTYCGESSAS NLTMANVPWH EEVVHFVQEL ADLIPDYEIA CEHEHSNCLL
IAHKKVRL
//
