TYW4_YEAST
ID TYW4_YEAST Reviewed; 695 AA.
AC Q08282; D6W1S8;
DT 07-MAR-2006, integrated into UniProtKB/Swiss-Prot.
DT 21-SEP-2011, sequence version 2.
DT 03-AUG-2022, entry version 153.
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=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=YOL141W;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169874;
RA Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J.,
RA Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A.,
RA Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B.,
RA Dang V.-D., de Haan M., Delius H., Durand P., Fairhead C., Feldmann H.,
RA Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E.,
RA Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U.,
RA Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B.,
RA Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A.,
RA Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C.,
RA Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G.,
RA Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B.,
RA Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B.,
RA Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F.,
RA Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E.,
RA Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I.,
RA Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H.,
RA Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV.";
RL Nature 387:98-102(1997).
RN [2]
RP GENOME REANNOTATION, AND SEQUENCE REVISION TO 417.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [3]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [4]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14576278; DOI=10.1073/pnas.2135385100;
RA Sickmann A., Reinders J., Wagner Y., Joppich C., Zahedi R.P., Meyer H.E.,
RA Schoenfisch B., Perschil I., Chacinska A., Guiard B., Rehling P.,
RA Pfanner N., Meisinger C.;
RT "The proteome of Saccharomyces cerevisiae mitochondria.";
RL Proc. Natl. Acad. Sci. U.S.A. 100:13207-13212(2003).
RN [5]
RP FUNCTION.
RX PubMed=16642040; DOI=10.1038/sj.emboj.7601105;
RA Noma A., Kirino Y., Ikeuchi Y., Suzuki T.;
RT "Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic
RT phenylalanine tRNA.";
RL EMBO J. 25:2142-2154(2006).
RN [6]
RP FUNCTION.
RX PubMed=17150819; DOI=10.1093/nass/nrl032;
RA Noma A., Suzuki T.;
RT "Ribonucleome analysis identified enzyme genes responsible for wybutosine
RT synthesis.";
RL Nucleic Acids Symp. Ser. 50:65-66(2006).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEXES WITH
RP S-ADENOSYL-L-METHIONINE AND S-ADENOSYL-L-HOMOCYSTEINE, FUNCTION, CATALYTIC
RP ACTIVITY, ACTIVE SITES, AND MUTAGENESIS OF ARG-88.
RX PubMed=19287006; DOI=10.1093/nar/gkp158;
RA Suzuki Y., Noma A., Suzuki T., Ishitani R., Nureki O.;
RT "Structural basis of tRNA modification with CO2 fixation and methylation by
RT wybutosine synthesizing enzyme TYW4.";
RL Nucleic Acids Res. 37:2910-2925(2009).
CC -!- FUNCTION: S-adenosyl-L-methionine-dependent methyltransferase that acts
CC as a component of the wybutosine biosynthesis pathway. Wybutosine is a
CC hyper modified guanosine with a tricyclic base found at the 3'-position
CC adjacent to the anticodon of eukaryotic phenylalanine tRNA. Catalyzes
CC the final 2 independent reactions, methylation of the alpha-carboxy
CC group of wybutosine-72 to form wybutosine-58, and methoxycarbonylation
CC of alpha-amino group of wybutosine-58 through the fixation of CO(2) to
CC complete wybutosine. {ECO:0000269|PubMed:16642040,
CC ECO:0000269|PubMed:17150819, ECO:0000269|PubMed:19287006}.
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 Evidence={ECO:0000269|PubMed:19287006};
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 Evidence={ECO:0000269|PubMed:19287006};
CC -!- PATHWAY: tRNA modification; wybutosine-tRNA(Phe) biosynthesis.
CC -!- SUBCELLULAR LOCATION: Cytoplasm. Mitochondrion.
CC -!- SIMILARITY: Belongs to the methyltransferase superfamily. LCMT family.
CC {ECO:0000305}.
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DR EMBL; Z74883; CAA99162.1; -; Genomic_DNA.
DR EMBL; BK006948; DAA10644.2; -; Genomic_DNA.
DR PIR; S61873; S61873.
DR RefSeq; NP_014500.2; NM_001183395.2.
DR PDB; 2ZW9; X-ray; 2.50 A; A/B=1-695.
DR PDB; 2ZWA; X-ray; 1.70 A; A/B=1-695.
DR PDB; 2ZZK; X-ray; 2.71 A; A/B=1-695.
DR PDBsum; 2ZW9; -.
DR PDBsum; 2ZWA; -.
DR PDBsum; 2ZZK; -.
DR AlphaFoldDB; Q08282; -.
DR SMR; Q08282; -.
DR BioGRID; 34276; 48.
DR IntAct; Q08282; 1.
DR STRING; 4932.YOL141W; -.
DR MaxQB; Q08282; -.
DR PaxDb; Q08282; -.
DR PRIDE; Q08282; -.
DR EnsemblFungi; YOL141W_mRNA; YOL141W; YOL141W.
DR GeneID; 854024; -.
DR KEGG; sce:YOL141W; -.
DR SGD; S000005501; PPM2.
DR VEuPathDB; FungiDB:YOL141W; -.
DR eggNOG; KOG2918; Eukaryota.
DR GeneTree; ENSGT00940000162599; -.
DR HOGENOM; CLU_002761_0_0_1; -.
DR InParanoid; Q08282; -.
DR OMA; WEVDFPD; -.
DR BioCyc; MetaCyc:YOL141W-MON; -.
DR BioCyc; YEAST:YOL141W-MON; -.
DR BRENDA; 2.1.1.290; 984.
DR BRENDA; 2.3.1.231; 984.
DR UniPathway; UPA00375; -.
DR EvolutionaryTrace; Q08282; -.
DR PRO; PR:Q08282; -.
DR Proteomes; UP000002311; Chromosome XV.
DR RNAct; Q08282; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0005739; C:mitochondrion; HDA:SGD.
DR GO; GO:0008175; F:tRNA methyltransferase activity; IDA:SGD.
DR GO; GO:0030488; P:tRNA methylation; IDA:SGD.
DR GO; GO:0006400; P:tRNA modification; TAS:Reactome.
DR GO; GO:0031591; P:wybutosine biosynthetic process; IMP:SGD.
DR Gene3D; 2.120.10.80; -; 1.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR011043; Gal_Oxase/kelch_b-propeller.
DR InterPro; IPR015915; Kelch-typ_b-propeller.
DR InterPro; IPR006652; Kelch_1.
DR InterPro; IPR007213; Ppm1/Ppm2/Tcmp.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR Pfam; PF04072; LCM; 1.
DR SMART; SM00612; Kelch; 1.
DR SUPFAM; SSF50965; SSF50965; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Methyltransferase; Mitochondrion;
KW Reference proteome; S-adenosyl-L-methionine; Transferase; tRNA processing.
FT CHAIN 1..695
FT /note="tRNA wybutosine-synthesizing protein 4"
FT /id="PRO_0000226146"
FT ACT_SITE 88
FT /note="Proton donor; for both methylation and
FT methoxycarbonylation activities"
FT /evidence="ECO:0000269|PubMed:19287006"
FT ACT_SITE 229
FT /note="Proton acceptor; for methoxycarbonylation activity"
FT /evidence="ECO:0000305|PubMed:19287006"
FT BINDING 38
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 88
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 115
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 146..147
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 196..197
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 224
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT MUTAGEN 88
FT /note="R->A: Loss of function."
FT /evidence="ECO:0000269|PubMed:19287006"
FT CONFLICT 417
FT /note="L -> M (in Ref. 1; CAA99162)"
FT /evidence="ECO:0000305"
FT HELIX 7..10
FT /evidence="ECO:0007829|PDB:2ZWA"
FT HELIX 17..28
FT /evidence="ECO:0007829|PDB:2ZWA"
FT HELIX 30..44
FT /evidence="ECO:0007829|PDB:2ZWA"
FT HELIX 46..48
FT /evidence="ECO:0007829|PDB:2ZWA"
FT HELIX 51..53
FT /evidence="ECO:0007829|PDB:2ZWA"
FT HELIX 67..70
FT /evidence="ECO:0007829|PDB:2ZWA"
FT HELIX 79..102
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 107..115
FT /evidence="ECO:0007829|PDB:2ZWA"
FT HELIX 121..126
FT /evidence="ECO:0007829|PDB:2ZWA"
FT HELIX 131..136
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 137..146
FT /evidence="ECO:0007829|PDB:2ZWA"
FT HELIX 148..160
FT /evidence="ECO:0007829|PDB:2ZWA"
FT HELIX 162..167
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 188..194
FT /evidence="ECO:0007829|PDB:2ZWA"
FT HELIX 200..209
FT /evidence="ECO:0007829|PDB:2ZWA"
FT TURN 210..213
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 217..226
FT /evidence="ECO:0007829|PDB:2ZWA"
FT HELIX 227..229
FT /evidence="ECO:0007829|PDB:2ZWA"
FT HELIX 232..243
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 245..255
FT /evidence="ECO:0007829|PDB:2ZWA"
FT HELIX 264..275
FT /evidence="ECO:0007829|PDB:2ZWA"
FT HELIX 282..284
FT /evidence="ECO:0007829|PDB:2ZWA"
FT HELIX 289..298
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 303..308
FT /evidence="ECO:0007829|PDB:2ZWA"
FT HELIX 309..315
FT /evidence="ECO:0007829|PDB:2ZWA"
FT HELIX 318..326
FT /evidence="ECO:0007829|PDB:2ZWA"
FT HELIX 333..341
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 343..350
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 352..354
FT /evidence="ECO:0007829|PDB:2ZW9"
FT TURN 358..360
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 375..381
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 392..395
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 400..403
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 406..410
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 414..419
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 424..428
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 444..448
FT /evidence="ECO:0007829|PDB:2ZWA"
FT TURN 449..452
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 453..457
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 460..462
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 471..474
FT /evidence="ECO:0007829|PDB:2ZWA"
FT TURN 475..478
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 479..482
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 490..492
FT /evidence="ECO:0007829|PDB:2ZW9"
FT STRAND 494..497
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 503..506
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 509..512
FT /evidence="ECO:0007829|PDB:2ZW9"
FT STRAND 514..519
FT /evidence="ECO:0007829|PDB:2ZWA"
FT TURN 520..523
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 524..527
FT /evidence="ECO:0007829|PDB:2ZWA"
FT HELIX 533..536
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 539..541
FT /evidence="ECO:0007829|PDB:2ZW9"
FT STRAND 543..547
FT /evidence="ECO:0007829|PDB:2ZWA"
FT TURN 548..551
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 552..556
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 569..575
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 584..591
FT /evidence="ECO:0007829|PDB:2ZWA"
FT HELIX 593..595
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 601..606
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 609..613
FT /evidence="ECO:0007829|PDB:2ZWA"
FT TURN 624..626
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 627..632
FT /evidence="ECO:0007829|PDB:2ZWA"
FT TURN 633..636
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 637..640
FT /evidence="ECO:0007829|PDB:2ZWA"
FT HELIX 645..650
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 659..661
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 668..671
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 674..676
FT /evidence="ECO:0007829|PDB:2ZWA"
FT HELIX 677..679
FT /evidence="ECO:0007829|PDB:2ZZK"
FT STRAND 682..684
FT /evidence="ECO:0007829|PDB:2ZWA"
FT STRAND 688..692
FT /evidence="ECO:0007829|PDB:2ZWA"
SQ SEQUENCE 695 AA; 78957 MW; DA38BE0B9ED7B357 CRC64;
MKNLTTIKQT NKNVKQERRK KYADLAIQGT NNSSIASKRS VELLYLPKLS SANNFQMDKN
NKLLEYFKFF VPKKIKRSPC INRGYWLRLF AIRSRLNSII EQTPQDKKIV VVNLGCGYDP
LPFQLLDTNN IQSQQYHDRV SFIDIDYSDL LKIKIELIKT IPELSKIIGL SEDKDYVDDS
NVDFLTTPKY LARPCDLNDS KMFSTLLNEC QLYDPNVVKV FVAEVSLAYM KPERSDSIIE
ATSKMENSHF IILEQLIPKG PFEPFSKQML AHFKRNDSPL QSVLKYNTIE SQVQRFNKLG
FAYVNVGDMF QLWESADEAT KKELLKVEPF DELEEFHLFC HHYVLCHATN YKEFAFTQGF
LFDRSISEIN LTVDEDYQLL ECECPINRKF GDVDVAGNDV FYMGGSNPYR VNEILQLSIH
YDKIDMKNIE VSSSEVPVAR MCHTFTTISR NNQLLLIGGR KAPHQGLSDN WIFDMKTREW
SMIKSLSHTR FRHSACSLPD GNVLILGGVT EGPAMLLYNV TEEIFKDVTP KDEFFQNSLV
SAGLEFDPVS KQGIILGGGF MDQTTVSDKA IIFKYDAENA TEPITVIKKL QHPLFQRYGS
QIKYITPRKL LIVGGTSPSG LFDRTNSIIS LDPLSETLTS IPISRRIWED HSLMLAGFSL
VSTSMGTIHI IGGGATCYGF GSVTNVGLKL IAIAK
