ID I1PFZ5_ORYGL Unreviewed; 653 AA.
AC I1PFZ5;
DT 13-JUN-2012, integrated into UniProtKB/TrEMBL.
DT 13-JUN-2012, sequence version 1.
DT 27-MAR-2024, entry version 50.
DE RecName: Full=tRNA 4-demethylwyosine synthase (AdoMet-dependent) {ECO:0000256|ARBA:ARBA00012821};
DE EC=4.1.3.44 {ECO:0000256|ARBA:ARBA00012821};
OS Oryza glaberrima (African rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza.
OX NCBI_TaxID=4538 {ECO:0000313|EnsemblPlants:ORGLA03G0329100.1, ECO:0000313|Proteomes:UP000007306};
RN [1] {ECO:0000313|Proteomes:UP000007306}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=IRGC 96717 {ECO:0000313|Proteomes:UP000007306};
RA Wing R.A., Yu Y., Rounsley S., Reddy-Marri P., Goicoechea J.L.,
RA Sisneros N., Lee S., Song X., Angelova A., Kudrna D.P., de Baynast K.,
RA Zuccolo A.;
RT "The complete genome of Oryza glaberrima.";
RL Submitted (JUN-2010) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EnsemblPlants:ORGLA03G0329100.1}
RP IDENTIFICATION.
RG EnsemblPlants;
RL Submitted (JUN-2015) 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}.
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DR AlphaFoldDB; I1PFZ5; -.
DR STRING; 4538.I1PFZ5; -.
DR EnsemblPlants; ORGLA03G0329100.1; ORGLA03G0329100.1; ORGLA03G0329100.
DR Gramene; ORGLA03G0329100.1; ORGLA03G0329100.1; ORGLA03G0329100.
DR eggNOG; KOG1160; Eukaryota.
DR HOGENOM; CLU_007952_2_0_1; -.
DR OMA; EWWTWIN; -.
DR UniPathway; UPA00375; -.
DR Proteomes; UP000007306; Chromosome 3.
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 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};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723};
KW S-adenosyl-L-methionine {ECO:0000256|ARBA:ARBA00022691}.
FT DOMAIN 56..204
FT /note="Flavodoxin-like"
FT /evidence="ECO:0000259|PROSITE:PS50902"
FT DOMAIN 324..567
FT /note="Radical SAM core"
FT /evidence="ECO:0000259|PROSITE:PS51918"
FT REGION 211..276
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 630..653
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 221..245
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 246..260
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 634..653
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 653 AA; 71465 MW; 83AD1AAF3319CCB0 CRC64;
MPPPFPTATA AASTTSHLAL LLLLSSSSVF FLYKSLRLRR NNPPSPPPGQ GPAPTPTLLY
ASATGTSKAL AAGLSRRLAE AVVTAHPADA AAFDPDDLPS LPLLLLVLPT HDGGAPPPAA
AFLARWLEES AADFRAGAAL LSGLRFAVFG VGSRAYGETF NAAARSFSRW LRALGAAEVV
AVGEGDVDGG DLEVVFEEWC GRVVRVVKGE EIGEGHNGES DGFDELEEEE SDDDDDEEEV
DGGEVDMEDI AGKAPAARRR NGKVEGALSN GGENGVRDMV TPIIRTSLEK QGYKIIGSHS
GVKICRWTKS QLRGRGGCYK HSFYGIESHR CMEATPSLAC ANKCVFCWRH HTNPVGKSWK
WKMDDPLDIV NAAIDQHTKM VKQMKGVPGV KPERLAEGLS PRHCALSLVG EPIMYPEINV
LIDELHRRHI STFLVTNAQF PDKIKTLKPI TQLYVSVDAA TKESLKAVDR PLFSDFWERF
LDSLKSLHDK DQRTVYRLTL VKGWNAEEID GYAKLLSLGQ PDFIEIKGVT YCGSSATSKL
TMENVPWHSD VKDFSEALAL KSGGVYEVAC EHAHSCCVLL AKVDKFKING KWHTWIDYDR
FHELVTSGKP FRSQDYMALT PSWAVYGAEE GGFDPDQSRY KKERRHGAAA LKD
//
