TYW4_YARLI
ID TYW4_YARLI Reviewed; 989 AA.
AC Q6C3P4;
DT 07-MAR-2006, integrated into UniProtKB/Swiss-Prot.
DT 16-AUG-2004, sequence version 1.
DT 03-AUG-2022, entry version 95.
DE RecName: Full=tRNA wybutosine-synthesizing protein 4;
DE Short=tRNA-yW synthesizing protein 4;
DE EC=2.1.1.290;
DE EC=2.3.1.231;
DE AltName: Full=Leucine carboxyl methyltransferase 2;
DE AltName: Full=tRNA(Phe) (7-(3-amino-3-(methoxycarbonyl)propyl)wyosine(37)-N)-methoxycarbonyltransferase;
DE AltName: Full=tRNA(Phe) (7-(3-amino-3-carboxypropyl)wyosine(37)-O)-methyltransferase;
GN Name=PPM2; Synonyms=TYW4; OrderedLocusNames=YALI0E33209g;
OS Yarrowia lipolytica (strain CLIB 122 / E 150) (Yeast) (Candida lipolytica).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Dipodascaceae; Yarrowia.
OX NCBI_TaxID=284591;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CLIB 122 / E 150;
RX PubMed=15229592; DOI=10.1038/nature02579;
RA Dujon B., Sherman D., Fischer G., Durrens P., Casaregola S., Lafontaine I.,
RA de Montigny J., Marck C., Neuveglise C., Talla E., Goffard N., Frangeul L.,
RA Aigle M., Anthouard V., Babour A., Barbe V., Barnay S., Blanchin S.,
RA Beckerich J.-M., Beyne E., Bleykasten C., Boisrame A., Boyer J.,
RA Cattolico L., Confanioleri F., de Daruvar A., Despons L., Fabre E.,
RA Fairhead C., Ferry-Dumazet H., Groppi A., Hantraye F., Hennequin C.,
RA Jauniaux N., Joyet P., Kachouri R., Kerrest A., Koszul R., Lemaire M.,
RA Lesur I., Ma L., Muller H., Nicaud J.-M., Nikolski M., Oztas S.,
RA Ozier-Kalogeropoulos O., Pellenz S., Potier S., Richard G.-F.,
RA Straub M.-L., Suleau A., Swennen D., Tekaia F., Wesolowski-Louvel M.,
RA Westhof E., Wirth B., Zeniou-Meyer M., Zivanovic Y., Bolotin-Fukuhara M.,
RA Thierry A., Bouchier C., Caudron B., Scarpelli C., Gaillardin C.,
RA Weissenbach J., Wincker P., Souciet J.-L.;
RT "Genome evolution in yeasts.";
RL Nature 430:35-44(2004).
CC -!- FUNCTION: Probable S-adenosyl-L-methionine-dependent methyltransferase
CC that acts as a 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. May methylate the carboxyl group of leucine residues to form
CC alpha-leucine ester residues (By similarity). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=7-[(3S)-3-amino-3-carboxypropyl]wyosine(37) in tRNA(Phe) + S-
CC adenosyl-L-methionine = 7-[(3S)-(3-amino-3-
CC methoxycarbonyl)propyl]wyosine(37) in tRNA(Phe) + S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:36903, Rhea:RHEA-COMP:10379, Rhea:RHEA-
CC COMP:11844, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:73543,
CC ChEBI:CHEBI:74275; EC=2.1.1.290;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=7-[(3S)-(3-amino-3-methoxycarbonyl)propyl]wyosine(37) in
CC tRNA(Phe) + CO2 + S-adenosyl-L-methionine = 2 H(+) + S-adenosyl-L-
CC homocysteine + wybutosine(37) in tRNA(Phe); Xref=Rhea:RHEA:37119,
CC Rhea:RHEA-COMP:11844, Rhea:RHEA-COMP:11847, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16526, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:73544, ChEBI:CHEBI:74275; EC=2.3.1.231;
CC -!- PATHWAY: tRNA modification; wybutosine-tRNA(Phe) biosynthesis.
CC -!- SIMILARITY: Belongs to the methyltransferase superfamily. LCMT family.
CC {ECO:0000305}.
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DR EMBL; CR382131; CAG80322.1; -; Genomic_DNA.
DR RefSeq; XP_504718.1; XM_504718.1.
DR AlphaFoldDB; Q6C3P4; -.
DR SMR; Q6C3P4; -.
DR STRING; 4952.CAG80322; -.
DR PRIDE; Q6C3P4; -.
DR EnsemblFungi; CAG80322; CAG80322; YALI0_E33209g.
DR GeneID; 2912958; -.
DR KEGG; yli:YALI0E33209g; -.
DR VEuPathDB; FungiDB:YALI0_E33209g; -.
DR HOGENOM; CLU_002761_1_0_1; -.
DR InParanoid; Q6C3P4; -.
DR OMA; WEVDFPD; -.
DR UniPathway; UPA00375; -.
DR Proteomes; UP000001300; Chromosome E.
DR GO; GO:0008175; F:tRNA methyltransferase activity; IBA:GO_Central.
DR GO; GO:0030488; P:tRNA methylation; IBA:GO_Central.
DR GO; GO:0031591; P:wybutosine biosynthetic process; IBA:GO_Central.
DR Gene3D; 2.120.10.80; -; 1.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR041667; Cupin_8.
DR InterPro; IPR011043; Gal_Oxase/kelch_b-propeller.
DR InterPro; IPR003347; JmjC_dom.
DR InterPro; IPR015915; Kelch-typ_b-propeller.
DR InterPro; IPR007213; Ppm1/Ppm2/Tcmp.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR Pfam; PF13621; Cupin_8; 1.
DR Pfam; PF04072; LCM; 1.
DR SMART; SM00558; JmjC; 1.
DR SUPFAM; SSF50965; SSF50965; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR PROSITE; PS51184; JMJC; 1.
PE 3: Inferred from homology;
KW Methyltransferase; Reference proteome; S-adenosyl-L-methionine;
KW Transferase; tRNA processing.
FT CHAIN 1..989
FT /note="tRNA wybutosine-synthesizing protein 4"
FT /id="PRO_0000226145"
FT DOMAIN 805..947
FT /note="JmjC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT REGION 1..42
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..24
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 102
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 127
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 153
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 202..203
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 233
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
SQ SEQUENCE 989 AA; 111174 MW; 0D8575C12057E1D7 CRC64;
MNGVTNDKGH SDVTNTPESG ISTPKKKNPK SDKPVKVKNP NNAASKAYTV DLKIQGTNNS
SIVSKRSVER LYKEKHDLEF FRHFVKKPQR RSPIINRGYW TRMEAMGYCI SAALAEKAPK
HVIVNLGCGY DPYPFQHLHK HGLTENLIFV DVDYPDLMQI KVDTIRRSDE LTKLVGEEKP
AAEIKDKSVL MQTGNYIALS CDLRDLEKFE FIFRNLDLIV EGDNNPLILF TAEVSVTYMF
QKDADNLLQW CASLPNSRFA LLEQIIPAGT EHPFAKTMLA HFDSLQTTLW SVKKYPSIPA
QYERFTCLGW KEVSGISLAQ FWDSYVPDEK KEFVENVEAF DEWEEFLLFL NHYSIIYGGA
DIFQNSKSEY PEHEEFVLQC EKPTSEAHRI GAAACSFQNG VILNGGQAQN RESTSLLLSL
DSTDEFIVDK NNMIARQYHS LSEIEPGVVL LAGGRSSPTK KFSDCHILKN GLWKPTFDLP
EGRFRHCMQG TLLFGGSESK DQWLHFSPTA GWKALKCDFH YLTPYGATLI MKSPIEGILL
GGMDAKGNLG KEVYSVTISE GETVVLSLIP MKSPLIYARY GAQGVYHGNR YLLVGGVSYD
ILFNEHNQVV ELDIKKGNTI PVKLPFESYP LLVSHSVNIV RNCLVVAGGG AVCFSFGVFH
SDPEVVGNRE LKVIKEQRPS EEVKTEINST VISVEEGTLE SFPAAYVNAT PTIFRNCDIG
PSSELWKSHD YLKSNIGEDT KVSVHIADNK NLNFQSKNFS YQTLQFGELM KLISDIEADS
ESSKSAYLRS LSLDNPKSEA TDLCKDFPGI ARDFKLPKEM ADFIGNKVFS TPLRISSSKT
QIWLHYDVTA NVLCQVTGSK RVRMYHPRDV VHLGFPAGES SSKIPNIFVH ESCAQAYEVV
MNPGDILFIP PMWLHAVEPQ TESISVNCFW KDLDGNKYSK TKDIYGNKDL ASYESGREGI
KKIADKFAGL PADIKEFYLR RLAEELKQM
