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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)DescriptionActionsGraphical viewLength
Binding sitei38S-adenosyl-L-methionine1
Active sitei88Proton donor; for both methylation and methoxycarbonylation activities1 Publication1
Binding sitei88S-adenosyl-L-methionine1
Binding sitei115S-adenosyl-L-methionine; via carbonyl oxygen1
Binding sitei224S-adenosyl-L-methionine1
Active sitei229Proton acceptor; for methoxycarbonylation activity1 Publication1

GO - Molecular functioni

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)DescriptionActionsGraphical viewLength
Mutagenesisi88R → A: Loss of function. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002261461 – 695tRNA wybutosine-synthesizing protein 4Add BLAST695

Proteomic databases

MaxQBiQ08282.
PRIDEiQ08282.

Interactioni

Protein-protein interaction databases

BioGridi34276. 10 interactors.
IntActiQ08282. 1 interactor.
MINTiMINT-4502250.

Structurei

Secondary structure

1695
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi7 – 10Combined sources4
Helixi17 – 28Combined sources12
Helixi30 – 44Combined sources15
Helixi46 – 48Combined sources3
Helixi51 – 53Combined sources3
Helixi67 – 70Combined sources4
Helixi79 – 102Combined sources24
Beta strandi107 – 115Combined sources9
Helixi121 – 126Combined sources6
Helixi131 – 136Combined sources6
Beta strandi137 – 146Combined sources10
Helixi148 – 160Combined sources13
Helixi162 – 167Combined sources6
Beta strandi188 – 194Combined sources7
Helixi200 – 209Combined sources10
Turni210 – 213Combined sources4
Beta strandi217 – 226Combined sources10
Helixi227 – 229Combined sources3
Helixi232 – 243Combined sources12
Beta strandi245 – 255Combined sources11
Helixi264 – 275Combined sources12
Helixi282 – 284Combined sources3
Helixi289 – 298Combined sources10
Beta strandi303 – 308Combined sources6
Helixi309 – 315Combined sources7
Helixi318 – 326Combined sources9
Helixi333 – 341Combined sources9
Beta strandi343 – 350Combined sources8
Beta strandi352 – 354Combined sources3
Turni358 – 360Combined sources3
Beta strandi375 – 381Combined sources7
Beta strandi392 – 395Combined sources4
Beta strandi400 – 403Combined sources4
Beta strandi406 – 410Combined sources5
Beta strandi414 – 419Combined sources6
Beta strandi424 – 428Combined sources5
Beta strandi444 – 448Combined sources5
Turni449 – 452Combined sources4
Beta strandi453 – 457Combined sources5
Beta strandi460 – 462Combined sources3
Beta strandi471 – 474Combined sources4
Turni475 – 478Combined sources4
Beta strandi479 – 482Combined sources4
Beta strandi490 – 492Combined sources3
Beta strandi494 – 497Combined sources4
Beta strandi503 – 506Combined sources4
Beta strandi509 – 512Combined sources4
Beta strandi514 – 519Combined sources6
Turni520 – 523Combined sources4
Beta strandi524 – 527Combined sources4
Helixi533 – 536Combined sources4
Beta strandi539 – 541Combined sources3
Beta strandi543 – 547Combined sources5
Turni548 – 551Combined sources4
Beta strandi552 – 556Combined sources5
Beta strandi569 – 575Combined sources7
Beta strandi584 – 591Combined sources8
Helixi593 – 595Combined sources3
Beta strandi601 – 606Combined sources6
Beta strandi609 – 613Combined sources5
Turni624 – 626Combined sources3
Beta strandi627 – 632Combined sources6
Turni633 – 636Combined sources4
Beta strandi637 – 640Combined sources4
Helixi645 – 650Combined sources6
Beta strandi659 – 661Combined sources3
Beta strandi668 – 671Combined sources4
Beta strandi674 – 676Combined sources3
Helixi677 – 679Combined sources3
Beta strandi682 – 684Combined sources3
Beta strandi688 – 692Combined sources5

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiQ08282.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni146 – 147S-adenosyl-L-methionine binding2
Regioni196 – 197S-adenosyl-L-methionine binding2

Sequence similaritiesi

Phylogenomic databases

GeneTreeiENSGT00530000063793.
HOGENOMiHOG000246544.
InParanoidiQ08282.
KOiK15451.
OMAiHFLILEQ.
OrthoDBiEOG092C0IJS.

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)DescriptionActionsGraphical viewLength
Sequence conflicti417L → M in CAA99162 (PubMed:9169874).Curated1

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2ZW9X-ray2.50A/B1-695[»]
2ZWAX-ray1.70A/B1-695[»]
2ZZKX-ray2.71A/B1-695[»]
ProteinModelPortaliQ08282.
SMRiQ08282.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34276. 10 interactors.
IntActiQ08282. 1 interactor.
MINTiMINT-4502250.

Proteomic databases

MaxQBiQ08282.
PRIDEiQ08282.

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.
OMAiHFLILEQ.
OrthoDBiEOG092C0IJS.

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...

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: November 2, 2016
This is version 119 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.