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tRNA wybutosine-synthesizing protein 4 (tRNA yW-synthesizing protein 4) (EC 2.1.1.290) (EC 2.3.1.231) (tRNA(Phe) (7-(3-amino-3-(methoxycarbonyl)propyl)wyosine(37)-N)-methoxycarbonyltransferase) (tRNA(Phe) (7-(3-amino-3-carboxypropyl)wyosine(37)-O)-methyltransferase)

 TYW4_YEAST              Reviewed;         695 AA.
Q08282; D6W1S8;
07-MAR-2006, integrated into UniProtKB/Swiss-Prot.
21-SEP-2011, sequence version 2.
28-MAR-2018, entry version 131.
RecName: Full=tRNA wybutosine-synthesizing protein 4;
Short=tRNA yW-synthesizing protein 4;
EC=2.1.1.290;
EC=2.3.1.231;
AltName: Full=tRNA(Phe) (7-(3-amino-3-(methoxycarbonyl)propyl)wyosine(37)-N)-methoxycarbonyltransferase;
AltName: Full=tRNA(Phe) (7-(3-amino-3-carboxypropyl)wyosine(37)-O)-methyltransferase;
Name=PPM2; Synonyms=TYW4; OrderedLocusNames=YOL141W;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9169874;
Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W.,
Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R.,
Boyer J., Camasses A., Casamayor A., Casas C., Cheret G.,
Cziepluch C., Daignan-Fornier B., Dang V.-D., de Haan M., Delius H.,
Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F.,
Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A.,
Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U.,
Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B.,
Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A.,
Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J.,
Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P.,
Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M.,
Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R.,
Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S.,
Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A.,
Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M.,
Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C.,
Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S.,
Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome XV.";
Nature 387:98-102(1997).
[2]
GENOME REANNOTATION, AND SEQUENCE REVISION TO 417.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[3]
SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
PubMed=14562095; DOI=10.1038/nature02026;
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
Weissman J.S., O'Shea E.K.;
"Global analysis of protein localization in budding yeast.";
Nature 425:686-691(2003).
[4]
SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
PubMed=14576278; DOI=10.1073/pnas.2135385100;
Sickmann A., Reinders J., Wagner Y., Joppich C., Zahedi R.P.,
Meyer H.E., Schoenfisch B., Perschil I., Chacinska A., Guiard B.,
Rehling P., Pfanner N., Meisinger C.;
"The proteome of Saccharomyces cerevisiae mitochondria.";
Proc. Natl. Acad. Sci. U.S.A. 100:13207-13212(2003).
[5]
FUNCTION.
PubMed=16642040; DOI=10.1038/sj.emboj.7601105;
Noma A., Kirino Y., Ikeuchi Y., Suzuki T.;
"Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic
phenylalanine tRNA.";
EMBO J. 25:2142-2154(2006).
[6]
FUNCTION.
PubMed=17150819; DOI=10.1093/nass/nrl032;
Noma A., Suzuki T.;
"Ribonucleome analysis identified enzyme genes responsible for
wybutosine synthesis.";
Nucleic Acids Symp. Ser. 50:65-66(2006).
[7]
X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEXES WITH
S-ADENOSYL-L-METHIONINE AND S-ADENOSYL-L-HOMOCYSTEINE, FUNCTION,
CATALYTIC ACTIVITY, ACTIVE SITES, AND MUTAGENESIS OF ARG-88.
PubMed=19287006; DOI=10.1093/nar/gkp158;
Suzuki Y., Noma A., Suzuki T., Ishitani R., Nureki O.;
"Structural basis of tRNA modification with CO2 fixation and
methylation by wybutosine synthesizing enzyme TYW4.";
Nucleic Acids Res. 37:2910-2925(2009).
-!- FUNCTION: S-adenosyl-L-methionine-dependent methyltransferase that
acts as a component of the wybutosine biosynthesis pathway.
Wybutosine is a hyper modified guanosine with a tricyclic base
found at the 3'-position adjacent to the anticodon of eukaryotic
phenylalanine tRNA. Catalyzes the final 2 independent reactions,
methylation of the alpha-carboxy group of wybutosine-72 to form
wybutosine-58, and methoxycarbonylation of alpha-amino group of
wybutosine-58 through the fixation of CO(2) to complete
wybutosine. {ECO:0000269|PubMed:16642040,
ECO:0000269|PubMed:17150819, ECO:0000269|PubMed:19287006}.
-!- CATALYTIC ACTIVITY: S-adenosyl-L-methionine + 7-((3S)-3-amino-3-
carboxypropyl)wyosine(37) in tRNA(Phe) = S-adenosyl-L-homocysteine
+ 7-((3S)-3-amino-3-(methoxycarbonyl)propyl)wyosine(37) in
tRNA(Phe). {ECO:0000269|PubMed:19287006}.
-!- CATALYTIC ACTIVITY: S-adenosyl-L-methionine + 7-((3S)-3-amino-3-
(methoxycarbonyl)propyl)wyosine(37) in tRNA(Phe) + CO(2) = S-
adenosyl-L-homocysteine + wybutosine(37) in tRNA(Phe).
{ECO:0000269|PubMed:19287006}.
-!- PATHWAY: tRNA modification; wybutosine-tRNA(Phe) biosynthesis.
-!- SUBCELLULAR LOCATION: Cytoplasm. Mitochondrion.
-!- SIMILARITY: Belongs to the methyltransferase superfamily. LCMT
family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; Z74883; CAA99162.1; -; Genomic_DNA.
EMBL; BK006948; DAA10644.2; -; Genomic_DNA.
PIR; S61873; S61873.
RefSeq; NP_014500.2; NM_001183395.2.
PDB; 2ZW9; X-ray; 2.50 A; A/B=1-695.
PDB; 2ZWA; X-ray; 1.70 A; A/B=1-695.
PDB; 2ZZK; X-ray; 2.71 A; A/B=1-695.
PDBsum; 2ZW9; -.
PDBsum; 2ZWA; -.
PDBsum; 2ZZK; -.
ProteinModelPortal; Q08282; -.
SMR; Q08282; -.
BioGrid; 34276; 44.
IntAct; Q08282; 5.
STRING; 4932.YOL141W; -.
MaxQB; Q08282; -.
PaxDb; Q08282; -.
PRIDE; Q08282; -.
EnsemblFungi; YOL141W; YOL141W; YOL141W.
GeneID; 854024; -.
KEGG; sce:YOL141W; -.
EuPathDB; FungiDB:YOL141W; -.
SGD; S000005501; PPM2.
GeneTree; ENSGT00530000063793; -.
HOGENOM; HOG000246544; -.
InParanoid; Q08282; -.
KO; K15451; -.
OMA; WDGRLYH; -.
OrthoDB; EOG092C0IJS; -.
BioCyc; MetaCyc:YOL141W-MONOMER; -.
BioCyc; YEAST:YOL141W-MONOMER; -.
BRENDA; 2.1.1.290; 984.
BRENDA; 2.3.1.231; 984.
UniPathway; UPA00375; -.
EvolutionaryTrace; Q08282; -.
PRO; PR:Q08282; -.
Proteomes; UP000002311; Chromosome XV.
GO; GO:0005737; C:cytoplasm; TAS:Reactome.
GO; GO:0005829; C:cytosol; IBA:GO_Central.
GO; GO:0005739; C:mitochondrion; IEA:UniProtKB-SubCell.
GO; GO:0008757; F:S-adenosylmethionine-dependent methyltransferase activity; IBA:GO_Central.
GO; GO:0008175; F:tRNA methyltransferase activity; IDA:SGD.
GO; GO:0030488; P:tRNA methylation; IDA:SGD.
GO; GO:0006400; P:tRNA modification; TAS:Reactome.
GO; GO:0031591; P:wybutosine biosynthetic process; IMP:SGD.
Gene3D; 2.120.10.80; -; 1.
InterPro; IPR011043; Gal_Oxase/kelch_b-propeller.
InterPro; IPR015915; Kelch-typ_b-propeller.
InterPro; IPR006652; Kelch_1.
InterPro; IPR007213; Ppm1/Ppm2/Tcmp.
InterPro; IPR029063; SAM-dependent_MTases.
Pfam; PF04072; LCM; 1.
SMART; SM00612; Kelch; 1.
SUPFAM; SSF50965; SSF50965; 1.
SUPFAM; SSF53335; SSF53335; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Cytoplasm; Methyltransferase;
Mitochondrion; Reference proteome; S-adenosyl-L-methionine;
Transferase; tRNA processing.
CHAIN 1 695 tRNA wybutosine-synthesizing protein 4.
/FTId=PRO_0000226146.
REGION 146 147 S-adenosyl-L-methionine binding.
REGION 196 197 S-adenosyl-L-methionine binding.
ACT_SITE 88 88 Proton donor; for both methylation and
methoxycarbonylation activities.
{ECO:0000269|PubMed:19287006}.
ACT_SITE 229 229 Proton acceptor; for methoxycarbonylation
activity. {ECO:0000305|PubMed:19287006}.
BINDING 38 38 S-adenosyl-L-methionine.
BINDING 88 88 S-adenosyl-L-methionine.
BINDING 115 115 S-adenosyl-L-methionine; via carbonyl
oxygen.
BINDING 224 224 S-adenosyl-L-methionine.
MUTAGEN 88 88 R->A: Loss of function.
{ECO:0000269|PubMed:19287006}.
CONFLICT 417 417 L -> M (in Ref. 1; CAA99162).
{ECO:0000305}.
HELIX 7 10 {ECO:0000244|PDB:2ZWA}.
HELIX 17 28 {ECO:0000244|PDB:2ZWA}.
HELIX 30 44 {ECO:0000244|PDB:2ZWA}.
HELIX 46 48 {ECO:0000244|PDB:2ZWA}.
HELIX 51 53 {ECO:0000244|PDB:2ZWA}.
HELIX 67 70 {ECO:0000244|PDB:2ZWA}.
HELIX 79 102 {ECO:0000244|PDB:2ZWA}.
STRAND 107 115 {ECO:0000244|PDB:2ZWA}.
HELIX 121 126 {ECO:0000244|PDB:2ZWA}.
HELIX 131 136 {ECO:0000244|PDB:2ZWA}.
STRAND 137 146 {ECO:0000244|PDB:2ZWA}.
HELIX 148 160 {ECO:0000244|PDB:2ZWA}.
HELIX 162 167 {ECO:0000244|PDB:2ZWA}.
STRAND 188 194 {ECO:0000244|PDB:2ZWA}.
HELIX 200 209 {ECO:0000244|PDB:2ZWA}.
TURN 210 213 {ECO:0000244|PDB:2ZWA}.
STRAND 217 226 {ECO:0000244|PDB:2ZWA}.
HELIX 227 229 {ECO:0000244|PDB:2ZWA}.
HELIX 232 243 {ECO:0000244|PDB:2ZWA}.
STRAND 245 255 {ECO:0000244|PDB:2ZWA}.
HELIX 264 275 {ECO:0000244|PDB:2ZWA}.
HELIX 282 284 {ECO:0000244|PDB:2ZWA}.
HELIX 289 298 {ECO:0000244|PDB:2ZWA}.
STRAND 303 308 {ECO:0000244|PDB:2ZWA}.
HELIX 309 315 {ECO:0000244|PDB:2ZWA}.
HELIX 318 326 {ECO:0000244|PDB:2ZWA}.
HELIX 333 341 {ECO:0000244|PDB:2ZWA}.
STRAND 343 350 {ECO:0000244|PDB:2ZWA}.
STRAND 352 354 {ECO:0000244|PDB:2ZW9}.
TURN 358 360 {ECO:0000244|PDB:2ZWA}.
STRAND 375 381 {ECO:0000244|PDB:2ZWA}.
STRAND 392 395 {ECO:0000244|PDB:2ZWA}.
STRAND 400 403 {ECO:0000244|PDB:2ZWA}.
STRAND 406 410 {ECO:0000244|PDB:2ZWA}.
STRAND 414 419 {ECO:0000244|PDB:2ZWA}.
STRAND 424 428 {ECO:0000244|PDB:2ZWA}.
STRAND 444 448 {ECO:0000244|PDB:2ZWA}.
TURN 449 452 {ECO:0000244|PDB:2ZWA}.
STRAND 453 457 {ECO:0000244|PDB:2ZWA}.
STRAND 460 462 {ECO:0000244|PDB:2ZWA}.
STRAND 471 474 {ECO:0000244|PDB:2ZWA}.
TURN 475 478 {ECO:0000244|PDB:2ZWA}.
STRAND 479 482 {ECO:0000244|PDB:2ZWA}.
STRAND 490 492 {ECO:0000244|PDB:2ZW9}.
STRAND 494 497 {ECO:0000244|PDB:2ZWA}.
STRAND 503 506 {ECO:0000244|PDB:2ZWA}.
STRAND 509 512 {ECO:0000244|PDB:2ZW9}.
STRAND 514 519 {ECO:0000244|PDB:2ZWA}.
TURN 520 523 {ECO:0000244|PDB:2ZWA}.
STRAND 524 527 {ECO:0000244|PDB:2ZWA}.
HELIX 533 536 {ECO:0000244|PDB:2ZWA}.
STRAND 539 541 {ECO:0000244|PDB:2ZW9}.
STRAND 543 547 {ECO:0000244|PDB:2ZWA}.
TURN 548 551 {ECO:0000244|PDB:2ZWA}.
STRAND 552 556 {ECO:0000244|PDB:2ZWA}.
STRAND 569 575 {ECO:0000244|PDB:2ZWA}.
STRAND 584 591 {ECO:0000244|PDB:2ZWA}.
HELIX 593 595 {ECO:0000244|PDB:2ZWA}.
STRAND 601 606 {ECO:0000244|PDB:2ZWA}.
STRAND 609 613 {ECO:0000244|PDB:2ZWA}.
TURN 624 626 {ECO:0000244|PDB:2ZWA}.
STRAND 627 632 {ECO:0000244|PDB:2ZWA}.
TURN 633 636 {ECO:0000244|PDB:2ZWA}.
STRAND 637 640 {ECO:0000244|PDB:2ZWA}.
HELIX 645 650 {ECO:0000244|PDB:2ZWA}.
STRAND 659 661 {ECO:0000244|PDB:2ZWA}.
STRAND 668 671 {ECO:0000244|PDB:2ZWA}.
STRAND 674 676 {ECO:0000244|PDB:2ZWA}.
HELIX 677 679 {ECO:0000244|PDB:2ZZK}.
STRAND 682 684 {ECO:0000244|PDB:2ZWA}.
STRAND 688 692 {ECO:0000244|PDB:2ZWA}.
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


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