TYW23_ORYSJ
ID TYW23_ORYSJ Reviewed; 1043 AA.
AC Q8H4D4; B9FXH9;
DT 03-APR-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 105.
DE RecName: Full=tRNA wybutosine-synthesizing protein 2/3/4;
DE Includes:
DE RecName: Full=tRNA wybutosine-synthesizing protein 3 homolog;
DE Short=tRNA-yW-synthesizing protein 3;
DE EC=2.1.1.282;
DE AltName: Full=tRNA(Phe) 7-((3-amino-3-carboxypropyl)-4-demethylwyosine(37)-N(4))-methyltransferase;
DE Includes:
DE RecName: Full=tRNA wybutosine-synthesizing protein 2 homolog;
DE Short=tRNA-yW-synthesizing protein 2;
DE EC=2.5.1.114;
DE AltName: Full=tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase;
GN OrderedLocusNames=Os07g0515000, LOC_Os07g33100;
GN ORFNames=OsJ_24443, P0048D08.111;
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=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 [2]
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 [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
CC -!- FUNCTION: S-adenosyl-L-methionine-dependent transferase that acts as a
CC component of the wybutosine biosynthesis pathway. Wybutosine is a hyper
CC modified guanosine with a tricyclic base found at the 3'-position
CC adjacent to the anticodon of eukaryotic phenylalanine tRNA (By
CC similarity). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=4-demethyl-7-[(3S)-3-amino-3-carboxypropyl]wyosine(37) in
CC tRNA(Phe) + S-adenosyl-L-methionine = 7-[(3S)-3-amino-3-
CC carboxypropyl]wyosine(37) in tRNA(Phe) + H(+) + S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:36635, Rhea:RHEA-COMP:10378, Rhea:RHEA-
CC COMP:10379, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:73543, ChEBI:CHEBI:73550; EC=2.1.1.282;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=4-demethylwyosine(37) in tRNA(Phe) + S-adenosyl-L-methionine =
CC 4-demethyl-7-[(3S)-3-amino-3-carboxypropyl]wyosine(37) in tRNA(Phe) +
CC H(+) + S-methyl-5'-thioadenosine; Xref=Rhea:RHEA:36355, Rhea:RHEA-
CC COMP:10164, Rhea:RHEA-COMP:10378, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:17509, ChEBI:CHEBI:59789, ChEBI:CHEBI:64315,
CC ChEBI:CHEBI:73550; EC=2.5.1.114;
CC -!- PATHWAY: tRNA modification; wybutosine-tRNA(Phe) biosynthesis.
CC -!- SIMILARITY: In the C-terminal section; belongs to the class I-like SAM-
CC binding methyltransferase superfamily. TRM5/TYW2 family. {ECO:0000305}.
CC -!- SIMILARITY: In the N-terminal section; belongs to the TYW3 family.
CC {ECO:0000305}.
CC -!- CAUTION: In plants, methylation steps 2, 3 and 4 of wybutosine
CC biosynthesis are probably processed by the this multifunctional enzyme,
CC while in other eukaryotes, these steps are mediated by 3 different
CC proteins. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAF21688.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=EEE67266.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AP004269; BAC20692.1; -; Genomic_DNA.
DR EMBL; AP008213; BAF21688.2; ALT_SEQ; Genomic_DNA.
DR EMBL; AP014963; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CM000144; EEE67266.1; ALT_SEQ; Genomic_DNA.
DR AlphaFoldDB; Q8H4D4; -.
DR SMR; Q8H4D4; -.
DR STRING; 39947.Q8H4D4; -.
DR PaxDb; Q8H4D4; -.
DR PRIDE; Q8H4D4; -.
DR HOGENOM; CLU_3227457_0_0_1; -.
DR InParanoid; Q8H4D4; -.
DR UniPathway; UPA00375; -.
DR Proteomes; UP000000763; Chromosome 7.
DR Proteomes; UP000007752; Chromosome 7.
DR Proteomes; UP000059680; Chromosome 7.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0102522; F:tRNA 4-demethylwyosine alpha-amino-alpha-carboxypropyltransferase activity; IEA:UniProtKB-EC.
DR GO; GO:0008175; F:tRNA methyltransferase activity; IBA:GO_Central.
DR GO; GO:0030488; P:tRNA methylation; IBA:GO_Central.
DR Gene3D; 2.120.10.80; -; 2.
DR Gene3D; 3.30.1960.10; -; 1.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR015915; Kelch-typ_b-propeller.
DR InterPro; IPR006652; Kelch_1.
DR InterPro; IPR030382; MeTrfase_TRM5/TYW2.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR InterPro; IPR003827; tRNA_yW-synthesising.
DR InterPro; IPR036602; tRNA_yW-synthesising-like_sf.
DR Pfam; PF01344; Kelch_1; 2.
DR Pfam; PF02475; Met_10; 1.
DR Pfam; PF02676; TYW3; 1.
DR SMART; SM00612; Kelch; 2.
DR SUPFAM; SSF111278; SSF111278; 1.
DR SUPFAM; SSF117281; SSF117281; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR PROSITE; PS51684; SAM_MT_TRM5_TYW2; 1.
PE 2: Evidence at transcript level;
KW Kelch repeat; Methyltransferase; Multifunctional enzyme;
KW Reference proteome; Repeat; S-adenosyl-L-methionine; Transferase;
KW tRNA processing.
FT CHAIN 1..1043
FT /note="tRNA wybutosine-synthesizing protein 2/3/4"
FT /id="PRO_0000281850"
FT REPEAT 360..410
FT /note="Kelch 1"
FT REPEAT 412..460
FT /note="Kelch 2"
FT REPEAT 461..510
FT /note="Kelch 3"
FT REPEAT 512..559
FT /note="Kelch 4"
FT REGION 1..233
FT /note="tRNA wybutosine-synthesizing protein 3 homolog"
FT REGION 53..75
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 700..1041
FT /note="tRNA wybutosine-synthesizing protein 2 homolog"
FT BINDING 874
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01021"
FT BINDING 942..943
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01021"
SQ SEQUENCE 1043 AA; 114471 MW; 7FC5AE9658033257 CRC64;
MEFDRRKAAA LAALASPAPD KSPKGGVDAP IAPLLDALNS HPDLFTTSSC SGRVSVLAQP
PPPQQADPGG AKTKKKARGG GWVYISHDPA DPEALVEVLF GVKEGGGGGD DELVFRFEPM
IVAVECRDAA AAAALVAAAV GAGFRESGIT SLQKRVMVAL RCSIRMEVPL GQTKELVVSP
DYIRYLVRIA NSKMEANKKR MGGFLDLLQA KISLEASYLE SQDPVLQNGA KHGFGNAKRH
VLISLSFYPA FISPHGVILT QEEALPTLSG NTTHCLSTAA LEITGEPIEK LFLWGQSACA
LTVGREHHIL TFGGFGGPGR HARRNYSLLV NPGSGLLTEL KVTGSPSPRM GHTITVVGND
IYVVGGRSGP SEILNDIWVL ERSNNRWSKV DCSGDFFRPR HRHAAAAVDR KVYVFGGLSD
DGLCSCMNIM DTASIQWNVI SPDDKWPCAR HSHSLVSYGS KLFLFGGHDG QRALNDFYSF
DTTTLKWNKE NTNGKAPSPR FSHCMFIYKD YLGILGGCPI RESSQEIALL NLKHKIWFYV
SIPSLSQCLC VRSSSVIIDD DLVIVGGGAS CYAFGTRFSQ PIKIDLHLLE SIFKLAYNKE
KEMSVQHGSV SNVDLLEGHE ENCNPSDNVK VVIDTATLGS SPLVLQLEKK YAKLAKDILK
KFGWLDLTRK VRVSQDNIHV LFPVSKTFHA LITDKHLKVQ PDDSCVFEEL LPFSENKLFG
ASISLQKALE ILLLCRGSIL KDEVAISRKA SKTPQTIMRE LVSVLLDKKG LPSQLLEQLP
TRWETLGDII VLPKTCFKDP LWESVRDDLW PLVAKSLGAQ RLARQGKITP NGTRDSTLEL
LVGNDGWLTH HENGICYSLD ATKCMFSSGN RSEKLRMGKL DCRDEVVVDL FAGIGYFVLP
FLVKANAKLV YACEWNPHAL EALQRNVMDN HVADRCIILE GDNRLTAPKG IADRVCLGLL
PSSECSWDTA VRALRAEGGM LHIHGNVNDS DESLWLDNVV KSITNIAKTH GLSWNVTVEH
VERVKWYGPH IRHLVVDVKC RAT
