Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

tRNA wybutosine-synthesizing protein 2

Gene

TRM12

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 transferase 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 transfer of the alpha-amino-alpha-carboxypropyl (acp) group from S-adenosyl-L-methionine to the C-7 position of 4-demethylwyosine (imG-14) to produce wybutosine-86.2 Publications

Catalytic activityi

S-adenosyl-L-methionine + 4-demethylwyosine(37) in tRNA(Phe) = S-methyl-5'-thioadenosine + 7-((3S)-3-amino-3-carboxypropyl)-4-demethylwyosine(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.3 Publications
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 sitei257 – 2571S-adenosyl-L-methioninePROSITE-ProRule annotation
Binding sitei264 – 2641S-adenosyl-L-methioninePROSITE-ProRule annotation

GO - Molecular functioni

  • S-adenosylmethionine-dependent methyltransferase activity Source: SGD
  • transferase activity, transferring alkyl or aryl (other than methyl) groups Source: SGD

GO - Biological processi

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

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

tRNA processing

Keywords - Ligandi

S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciMetaCyc:G3O-32610-MONOMER.
YEAST:G3O-32610-MONOMER.
BRENDAi2.5.1.114. 984.
ReactomeiR-SCE-6782861. Synthesis of wybutosine at G37 of tRNA(Phe).
UniPathwayiUPA00375.

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA wybutosine-synthesizing protein 2 (EC:2.5.1.114)
Short name:
tRNA-yW-synthesizing protein 2
Alternative name(s):
tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase
Gene namesi
Name:TRM12
Synonyms:TYW2
Ordered Locus Names:YML005W
ORF Names:YM9571.14
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XIII

Organism-specific databases

EuPathDBiFungiDB:YML005W.
SGDiS000004464. TRM12.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

tRNA(Phe) from mutant shows accumulation of 4-demethylwyosine (ImG-14) and absence of wybutosine.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 462462tRNA wybutosine-synthesizing protein 2PRO_0000203264Add
BLAST

Proteomic databases

MaxQBiQ04235.

Interactioni

Protein-protein interaction databases

BioGridi35166. 10 interactions.
MINTiMINT-2493038.

Structurei

3D structure databases

ProteinModelPortaliQ04235.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni305 – 3062S-adenosyl-L-methionine bindingPROSITE-ProRule annotation

Sequence similaritiesi

Belongs to the class I-like SAM-binding methyltransferase superfamily. TRM5/TYW2 family.PROSITE-ProRule annotation

Phylogenomic databases

GeneTreeiENSGT00390000006078.
HOGENOMiHOG000000750.
InParanoidiQ04235.
KOiK07055.
OMAiFELNPWS.
OrthoDBiEOG7M6DM1.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR030382. MeTrfase_TRM5/TYW2.
IPR029063. SAM-dependent_MTases.
IPR026274. tRNA_wybutosine_synth_prot_2.
[Graphical view]
PfamiPF02475. Met_10. 1 hit.
[Graphical view]
PIRSFiPIRSF038972. Trm12. 1 hit.
SUPFAMiSSF53335. SSF53335. 2 hits.
PROSITEiPS51684. SAM_MT_TRM5_TYW2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q04235-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSDETMPVEF LVSDKRLLKT IKVKLETNGL FVTPIYSDND NKVIKSSIED
60 70 80 90 100
LNHPLAVEIN NIAGVKARFH ESGNLERSEG HLKHQSNSIT EFTKSFLKDH
110 120 130 140 150
GLANDKIFLS HLLDHLPLKY TIYPPVVLFN NSTVRSFNHP IWQKAFQLKL
160 170 180 190 200
FDPNEYYREL LCFLSPGKPS KGTSLHPNNR LLTHLAINNP ITEADVLRRP
210 220 230 240 250
FNIQPLYGKL IDDSILDDND NTLWENPSQE QLNSSIWCKV IQNGVTQIWS
260 270 280 290 300
PVFTMFSRGN IKEKKRVLTT FPDICNNDVV DLYAGIGYFT FSYLTKGART
310 320 330 340 350
LFAFELNPWS VEGLKRGLKA NGFNKSGNCH VFQESNEMCV QRLTEFLSQN
360 370 380 390 400
PGFRLRIRHI NLGLLPSSKQ GWPLAIKLIY LQGASLEKVT MHIHENVHID
410 420 430 440 450
AIEDGSFEKN VIVELDAINE SIALIRNRGI KLQFVRSKLE RIKTFAPDIW
460
HVCVDVDVIV ST
Length:462
Mass (Da):52,726
Last modified:November 1, 1997 - v1
Checksum:iC581EF189A7D733C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z49810 Genomic DNA. Translation: CAA89947.1.
BK006946 Genomic DNA. Translation: DAA09894.1.
PIRiS55114.
RefSeqiNP_013709.1. NM_001182360.1.

Genome annotation databases

EnsemblFungiiYML005W; YML005W; YML005W.
GeneIDi855008.
KEGGisce:YML005W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z49810 Genomic DNA. Translation: CAA89947.1.
BK006946 Genomic DNA. Translation: DAA09894.1.
PIRiS55114.
RefSeqiNP_013709.1. NM_001182360.1.

3D structure databases

ProteinModelPortaliQ04235.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35166. 10 interactions.
MINTiMINT-2493038.

Proteomic databases

MaxQBiQ04235.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYML005W; YML005W; YML005W.
GeneIDi855008.
KEGGisce:YML005W.

Organism-specific databases

EuPathDBiFungiDB:YML005W.
SGDiS000004464. TRM12.

Phylogenomic databases

GeneTreeiENSGT00390000006078.
HOGENOMiHOG000000750.
InParanoidiQ04235.
KOiK07055.
OMAiFELNPWS.
OrthoDBiEOG7M6DM1.

Enzyme and pathway databases

UniPathwayiUPA00375.
BioCyciMetaCyc:G3O-32610-MONOMER.
YEAST:G3O-32610-MONOMER.
BRENDAi2.5.1.114. 984.
ReactomeiR-SCE-6782861. Synthesis of wybutosine at G37 of tRNA(Phe).

Miscellaneous databases

PROiQ04235.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR030382. MeTrfase_TRM5/TYW2.
IPR029063. SAM-dependent_MTases.
IPR026274. tRNA_wybutosine_synth_prot_2.
[Graphical view]
PfamiPF02475. Met_10. 1 hit.
[Graphical view]
PIRSFiPIRSF038972. Trm12. 1 hit.
SUPFAMiSSF53335. SSF53335. 2 hits.
PROSITEiPS51684. SAM_MT_TRM5_TYW2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  3. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  4. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  5. "A novel methyltransferase required for the formation of the hypermodified nucleoside wybutosine in eucaryotic tRNA."
    Kalhor H.R., Penjwini M., Clarke S.
    Biochem. Biophys. Res. Commun. 334:433-440(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: PATHWAY, DISRUPTION PHENOTYPE.
  6. "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, CATALYTIC ACTIVITY, PATHWAY.
  7. "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, PATHWAY.

Entry informationi

Entry nameiTYW2_YEAST
AccessioniPrimary (citable) accession number: Q04235
Secondary accession number(s): D6VZH0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: July 6, 2016
This is version 117 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 656 molecules/cell in log phase SD medium.1 Publication

Caution

Was originally thought to be a methyltransferase.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

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