TYW1_ORYSJ
ID TYW1_ORYSJ Reviewed; 653 AA.
AC Q8H8N3; Q0DN45;
DT 03-APR-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 113.
DE RecName: Full=S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase;
DE EC=4.1.3.44;
DE AltName: Full=tRNA wybutosine-synthesizing protein 1 homolog;
GN Name=TYW1; OrderedLocusNames=Os03g0775300, LOC_Os03g56390;
GN ORFNames=OSJNBa0070N04.14;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16109971; DOI=10.1101/gr.3869505;
RG The rice chromosome 3 sequencing consortium;
RA Buell C.R., Yuan Q., Ouyang S., Liu J., Zhu W., Wang A., Maiti R., Haas B.,
RA Wortman J., Pertea M., Jones K.M., Kim M., Overton L., Tsitrin T.,
RA Fadrosh D., Bera J., Weaver B., Jin S., Johri S., Reardon M., Webb K.,
RA Hill J., Moffat K., Tallon L., Van Aken S., Lewis M., Utterback T.,
RA Feldblyum T., Zismann V., Iobst S., Hsiao J., de Vazeille A.R.,
RA Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H., Rambo T., Currie J.,
RA Collura K., Kernodle-Thompson S., Wei F., Kudrna K., Ammiraju J.S.S.,
RA Luo M., Goicoechea J.L., Wing R.A., Henry D., Oates R., Palmer M.,
RA Pries G., Saski C., Simmons J., Soderlund C., Nelson W., de la Bastide M.,
RA Spiegel L., Nascimento L., Huang E., Preston R., Zutavern T., Palmer L.,
RA O'Shaughnessy A., Dike S., McCombie W.R., Minx P., Cordum H., Wilson R.,
RA Jin W., Lee H.R., Jiang J., Jackson S.;
RT "Sequence, annotation, and analysis of synteny between rice chromosome 3
RT and diverged grass species.";
RL Genome Res. 15:1284-1291(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
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 (By similarity). {ECO:0000250}.
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 -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883; Evidence={ECO:0000250};
CC Note=Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3
CC cysteines and an exchangeable S-adenosyl-L-methionine. {ECO:0000250};
CC -!- PATHWAY: tRNA modification; wybutosine-tRNA(Phe) biosynthesis.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q8H8N3-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8H8N3-2; Sequence=VSP_024072;
CC -!- SIMILARITY: Belongs to the TYW1 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AK100507; Type=Frameshift; Evidence={ECO:0000305};
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AC091494; AAN65027.1; -; Genomic_DNA.
DR EMBL; DP000009; ABF99122.1; -; Genomic_DNA.
DR EMBL; AP008209; BAF13343.1; -; Genomic_DNA.
DR EMBL; AP014959; BAS86627.1; -; Genomic_DNA.
DR EMBL; AK100507; -; NOT_ANNOTATED_CDS; mRNA.
DR RefSeq; XP_015631211.1; XM_015775725.1. [Q8H8N3-1]
DR AlphaFoldDB; Q8H8N3; -.
DR SMR; Q8H8N3; -.
DR STRING; 4530.OS03T0775300-01; -.
DR PaxDb; Q8H8N3; -.
DR PRIDE; Q8H8N3; -.
DR EnsemblPlants; Os03t0775300-01; Os03t0775300-01; Os03g0775300. [Q8H8N3-2]
DR GeneID; 4334285; -.
DR Gramene; Os03t0775300-01; Os03t0775300-01; Os03g0775300. [Q8H8N3-2]
DR KEGG; osa:4334285; -.
DR eggNOG; KOG1160; Eukaryota.
DR InParanoid; Q8H8N3; -.
DR OMA; REMITPM; -.
DR OrthoDB; 731783at2759; -.
DR UniPathway; UPA00375; -.
DR Proteomes; UP000000763; Chromosome 3.
DR Proteomes; UP000059680; 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:0016651; F:oxidoreductase activity, acting on NAD(P)H; IEA:UniProt.
DR GO; GO:0102521; F:tRNA-4-demethylwyosine synthase activity; IEA:UniProtKB-EC.
DR GO; GO:0031591; P:wybutosine biosynthetic process; IBA:GO_Central.
DR Gene3D; 3.20.20.70; -; 1.
DR Gene3D; 3.40.50.360; -; 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; PTHR13930; 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; SSF52218; 1.
DR PROSITE; PS50902; FLAVODOXIN_LIKE; 1.
DR PROSITE; PS51918; RADICAL_SAM; 1.
PE 2: Evidence at transcript level;
KW 4Fe-4S; Alternative splicing; Iron; Iron-sulfur; Lyase; Metal-binding;
KW Nucleotide-binding; Reference proteome; S-adenosyl-L-methionine;
KW tRNA processing.
FT CHAIN 1..653
FT /note="S-adenosyl-L-methionine-dependent tRNA 4-
FT demethylwyosine synthase"
FT /id="PRO_0000281833"
FT DOMAIN 56..204
FT /note="Flavodoxin-like"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00088"
FT DOMAIN 324..567
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
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"
FT BINDING 62..66
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00088"
FT BINDING 148..180
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00088"
FT BINDING 340
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255"
FT BINDING 344
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255"
FT BINDING 347
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255"
FT VAR_SEQ 110..162
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:12869764"
FT /id="VSP_024072"
SQ SEQUENCE 653 AA; 71423 MW; 7DADAAA8F9A5BA7A CRC64;
MPPPFPTATA AASTTSHLAL LLLLSSSSVF FLYKSLRLRR NNPPSPPPGQ GPAPTPTLLY
ASATGTSKAL AAGLSRRLAE AGVTAHPADA 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
