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Protein

tRNA wybutosine-synthesizing protein 4

Gene

PPM2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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 CO2 to complete wybutosine.3 Publications

Catalytic activityi

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).1 Publication
S-adenosyl-L-methionine + 7-((3S)-3-amino-3-(methoxycarbonyl)propyl)wyosine(37) in tRNA(Phe) + CO2 = S-adenosyl-L-homocysteine + wybutosine(37) in tRNA(Phe).1 Publication

Pathwayi: wybutosine-tRNA(Phe) biosynthesis

This protein is involved in the pathway wybutosine-tRNA(Phe) biosynthesis, which is part of tRNA modification.
View all proteins of this organism that are known to be involved in the pathway wybutosine-tRNA(Phe) biosynthesis and in tRNA modification.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei38 – 381S-adenosyl-L-methionine
Active sitei88 – 881Proton donor; for both methylation and methoxycarbonylation activities1 Publication
Binding sitei88 – 881S-adenosyl-L-methionine
Binding sitei115 – 1151S-adenosyl-L-methionine; via carbonyl oxygen
Binding sitei224 – 2241S-adenosyl-L-methionine
Active sitei229 – 2291Proton acceptor; for methoxycarbonylation activity1 Publication

GO - Molecular functioni

  • tRNA methyltransferase activity Source: SGD

GO - Biological processi

  • tRNA methylation Source: SGD
  • tRNA modification Source: Reactome
  • wybutosine biosynthetic process Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

tRNA processing

Keywords - Ligandi

S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciMetaCyc:YOL141W-MONOMER.
YEAST:YOL141W-MONOMER.
BRENDAi2.1.1.290. 984.
2.3.1.231. 984.
ReactomeiR-SCE-6782861. Synthesis of wybutosine at G37 of tRNA(Phe).
UniPathwayiUPA00375.

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA wybutosine-synthesizing protein 4 (EC:2.1.1.290, EC:2.3.1.231)
Short name:
tRNA yW-synthesizing protein 4
Alternative name(s):
tRNA(Phe) (7-(3-amino-3-(methoxycarbonyl)propyl)wyosine(37)-N)-methoxycarbonyltransferase
tRNA(Phe) (7-(3-amino-3-carboxypropyl)wyosine(37)-O)-methyltransferase
Gene namesi
Name:PPM2
Synonyms:TYW4
Ordered Locus Names:YOL141W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XV

Organism-specific databases

EuPathDBiFungiDB:YOL141W.
SGDiS000005501. PPM2.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Mitochondrion

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi88 – 881R → A: Loss of function. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 695695tRNA wybutosine-synthesizing protein 4PRO_0000226146Add
BLAST

Proteomic databases

MaxQBiQ08282.

Interactioni

Protein-protein interaction databases

BioGridi34276. 9 interactions.
IntActiQ08282. 1 interaction.
MINTiMINT-4502250.

Structurei

Secondary structure

1
695
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi7 – 104Combined sources
Helixi17 – 2812Combined sources
Helixi30 – 4415Combined sources
Helixi46 – 483Combined sources
Helixi51 – 533Combined sources
Helixi67 – 704Combined sources
Helixi79 – 10224Combined sources
Beta strandi107 – 1159Combined sources
Helixi121 – 1266Combined sources
Helixi131 – 1366Combined sources
Beta strandi137 – 14610Combined sources
Helixi148 – 16013Combined sources
Helixi162 – 1676Combined sources
Beta strandi188 – 1947Combined sources
Helixi200 – 20910Combined sources
Turni210 – 2134Combined sources
Beta strandi217 – 22610Combined sources
Helixi227 – 2293Combined sources
Helixi232 – 24312Combined sources
Beta strandi245 – 25511Combined sources
Helixi264 – 27512Combined sources
Helixi282 – 2843Combined sources
Helixi289 – 29810Combined sources
Beta strandi303 – 3086Combined sources
Helixi309 – 3157Combined sources
Helixi318 – 3269Combined sources
Helixi333 – 3419Combined sources
Beta strandi343 – 3508Combined sources
Beta strandi352 – 3543Combined sources
Turni358 – 3603Combined sources
Beta strandi375 – 3817Combined sources
Beta strandi392 – 3954Combined sources
Beta strandi400 – 4034Combined sources
Beta strandi406 – 4105Combined sources
Beta strandi414 – 4196Combined sources
Beta strandi424 – 4285Combined sources
Beta strandi444 – 4485Combined sources
Turni449 – 4524Combined sources
Beta strandi453 – 4575Combined sources
Beta strandi460 – 4623Combined sources
Beta strandi471 – 4744Combined sources
Turni475 – 4784Combined sources
Beta strandi479 – 4824Combined sources
Beta strandi490 – 4923Combined sources
Beta strandi494 – 4974Combined sources
Beta strandi503 – 5064Combined sources
Beta strandi509 – 5124Combined sources
Beta strandi514 – 5196Combined sources
Turni520 – 5234Combined sources
Beta strandi524 – 5274Combined sources
Helixi533 – 5364Combined sources
Beta strandi539 – 5413Combined sources
Beta strandi543 – 5475Combined sources
Turni548 – 5514Combined sources
Beta strandi552 – 5565Combined sources
Beta strandi569 – 5757Combined sources
Beta strandi584 – 5918Combined sources
Helixi593 – 5953Combined sources
Beta strandi601 – 6066Combined sources
Beta strandi609 – 6135Combined sources
Turni624 – 6263Combined sources
Beta strandi627 – 6326Combined sources
Turni633 – 6364Combined sources
Beta strandi637 – 6404Combined sources
Helixi645 – 6506Combined sources
Beta strandi659 – 6613Combined sources
Beta strandi668 – 6714Combined sources
Beta strandi674 – 6763Combined sources
Helixi677 – 6793Combined sources
Beta strandi682 – 6843Combined sources
Beta strandi688 – 6925Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2ZW9X-ray2.50A/B1-695[»]
2ZWAX-ray1.70A/B1-695[»]
2ZZKX-ray2.71A/B1-695[»]
ProteinModelPortaliQ08282.
SMRiQ08282. Positions 13-694.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ08282.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni146 – 1472S-adenosyl-L-methionine binding
Regioni196 – 1972S-adenosyl-L-methionine binding

Sequence similaritiesi

Phylogenomic databases

GeneTreeiENSGT00530000063793.
HOGENOMiHOG000246544.
InParanoidiQ08282.
KOiK15451.
OMAiEVSLAYM.
OrthoDBiEOG7K0ZP5.

Family and domain databases

Gene3Di2.120.10.80. 2 hits.
3.40.50.150. 1 hit.
InterProiIPR011043. Gal_Oxase/kelch_b-propeller.
IPR015915. Kelch-typ_b-propeller.
IPR006652. Kelch_1.
IPR007213. Ppm1/Ppm2/Tcmp.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PANTHERiPTHR13600. PTHR13600. 2 hits.
PfamiPF04072. LCM. 1 hit.
[Graphical view]
SMARTiSM00612. Kelch. 1 hit.
[Graphical view]
SUPFAMiSSF50965. SSF50965. 1 hit.
SSF53335. SSF53335. 1 hit.

Sequencei

Sequence statusi: Complete.

Q08282-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKNLTTIKQT NKNVKQERRK KYADLAIQGT NNSSIASKRS VELLYLPKLS
60 70 80 90 100
SANNFQMDKN NKLLEYFKFF VPKKIKRSPC INRGYWLRLF AIRSRLNSII
110 120 130 140 150
EQTPQDKKIV VVNLGCGYDP LPFQLLDTNN IQSQQYHDRV SFIDIDYSDL
160 170 180 190 200
LKIKIELIKT IPELSKIIGL SEDKDYVDDS NVDFLTTPKY LARPCDLNDS
210 220 230 240 250
KMFSTLLNEC QLYDPNVVKV FVAEVSLAYM KPERSDSIIE ATSKMENSHF
260 270 280 290 300
IILEQLIPKG PFEPFSKQML AHFKRNDSPL QSVLKYNTIE SQVQRFNKLG
310 320 330 340 350
FAYVNVGDMF QLWESADEAT KKELLKVEPF DELEEFHLFC HHYVLCHATN
360 370 380 390 400
YKEFAFTQGF LFDRSISEIN LTVDEDYQLL ECECPINRKF GDVDVAGNDV
410 420 430 440 450
FYMGGSNPYR VNEILQLSIH YDKIDMKNIE VSSSEVPVAR MCHTFTTISR
460 470 480 490 500
NNQLLLIGGR KAPHQGLSDN WIFDMKTREW SMIKSLSHTR FRHSACSLPD
510 520 530 540 550
GNVLILGGVT EGPAMLLYNV TEEIFKDVTP KDEFFQNSLV SAGLEFDPVS
560 570 580 590 600
KQGIILGGGF MDQTTVSDKA IIFKYDAENA TEPITVIKKL QHPLFQRYGS
610 620 630 640 650
QIKYITPRKL LIVGGTSPSG LFDRTNSIIS LDPLSETLTS IPISRRIWED
660 670 680 690
HSLMLAGFSL VSTSMGTIHI IGGGATCYGF GSVTNVGLKL IAIAK
Length:695
Mass (Da):78,957
Last modified:September 21, 2011 - v2
Checksum:iDA38BE0B9ED7B357
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti417 – 4171L → M in CAA99162 (PubMed:9169874).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z74883 Genomic DNA. Translation: CAA99162.1.
BK006948 Genomic DNA. Translation: DAA10644.2.
PIRiS61873.
RefSeqiNP_014500.2. NM_001183395.2.

Genome annotation databases

EnsemblFungiiYOL141W; YOL141W; YOL141W.
GeneIDi854024.
KEGGisce:YOL141W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z74883 Genomic DNA. Translation: CAA99162.1.
BK006948 Genomic DNA. Translation: DAA10644.2.
PIRiS61873.
RefSeqiNP_014500.2. NM_001183395.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2ZW9X-ray2.50A/B1-695[»]
2ZWAX-ray1.70A/B1-695[»]
2ZZKX-ray2.71A/B1-695[»]
ProteinModelPortaliQ08282.
SMRiQ08282. Positions 13-694.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34276. 9 interactions.
IntActiQ08282. 1 interaction.
MINTiMINT-4502250.

Proteomic databases

MaxQBiQ08282.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYOL141W; YOL141W; YOL141W.
GeneIDi854024.
KEGGisce:YOL141W.

Organism-specific databases

EuPathDBiFungiDB:YOL141W.
SGDiS000005501. PPM2.

Phylogenomic databases

GeneTreeiENSGT00530000063793.
HOGENOMiHOG000246544.
InParanoidiQ08282.
KOiK15451.
OMAiEVSLAYM.
OrthoDBiEOG7K0ZP5.

Enzyme and pathway databases

UniPathwayiUPA00375.
BioCyciMetaCyc:YOL141W-MONOMER.
YEAST:YOL141W-MONOMER.
BRENDAi2.1.1.290. 984.
2.3.1.231. 984.
ReactomeiR-SCE-6782861. Synthesis of wybutosine at G37 of tRNA(Phe).

Miscellaneous databases

EvolutionaryTraceiQ08282.
PROiQ08282.

Family and domain databases

Gene3Di2.120.10.80. 2 hits.
3.40.50.150. 1 hit.
InterProiIPR011043. Gal_Oxase/kelch_b-propeller.
IPR015915. Kelch-typ_b-propeller.
IPR006652. Kelch_1.
IPR007213. Ppm1/Ppm2/Tcmp.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PANTHERiPTHR13600. PTHR13600. 2 hits.
PfamiPF04072. LCM. 1 hit.
[Graphical view]
SMARTiSM00612. Kelch. 1 hit.
[Graphical view]
SUPFAMiSSF50965. SSF50965. 1 hit.
SSF53335. SSF53335. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV."
    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.
    Nature 387:98-102(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. Cited for: GENOME REANNOTATION, SEQUENCE REVISION TO 417.
    Strain: ATCC 204508 / S288c.
  3. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  4. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  5. "Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic phenylalanine tRNA."
    Noma A., Kirino Y., Ikeuchi Y., Suzuki T.
    EMBO J. 25:2142-2154(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  6. "Ribonucleome analysis identified enzyme genes responsible for wybutosine synthesis."
    Noma A., Suzuki T.
    Nucleic Acids Symp. Ser. 50:65-66(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  7. "Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4."
    Suzuki Y., Noma A., Suzuki T., Ishitani R., Nureki O.
    Nucleic Acids Res. 37:2910-2925(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEXES WITH S-ADENOSYL-L-METHIONINE AND S-ADENOSYL-L-HOMOCYSTEINE, FUNCTION, CATALYTIC ACTIVITY, ACTIVE SITES, MUTAGENESIS OF ARG-88.

Entry informationi

Entry nameiTYW4_YEAST
AccessioniPrimary (citable) accession number: Q08282
Secondary accession number(s): D6W1S8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 7, 2006
Last sequence update: September 21, 2011
Last modified: June 8, 2016
This is version 115 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
  4. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  5. Yeast chromosome XV
    Yeast (Saccharomyces cerevisiae) chromosome XV: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.