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Protein

tRNA wybutosine-synthesizing protein 2

Gene

TRM12

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: -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

Miscellaneous

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

Caution

Was originally thought to be a methyltransferase.1 Publication

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)DescriptionActionsGraphical viewLength
Binding sitei257S-adenosyl-L-methioninePROSITE-ProRule annotation1
Binding sitei264S-adenosyl-L-methioninePROSITE-ProRule annotation1

GO - Molecular functioni

GO - Biological processi

  • tRNA methylation Source: SGD
  • tRNA modification Source: Reactome
  • wybutosine biosynthetic process Source: SGD

Keywordsi

Molecular functionTransferase
Biological processtRNA processing
LigandS-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciMetaCyc:G3O-32610-MONOMER
YEAST:G3O-32610-MONOMER
BRENDAi2.5.1.114 984
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

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)DescriptionActionsGraphical viewLength
ChainiPRO_00002032641 – 462tRNA wybutosine-synthesizing protein 2Add BLAST462

Proteomic databases

MaxQBiQ04235
PaxDbiQ04235
PRIDEiQ04235

Interactioni

Protein-protein interaction databases

BioGridi35166, 75 interactors
MINTiQ04235
STRINGi4932.YML005W

Structurei

3D structure databases

ProteinModelPortaliQ04235
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni305 – 306S-adenosyl-L-methionine bindingPROSITE-ProRule annotation2

Sequence similaritiesi

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

Phylogenomic databases

GeneTreeiENSGT00390000006078
HOGENOMiHOG000000750
InParanoidiQ04235
KOiK07055
OMAiRFTIYEP
OrthoDBiEOG092C29GN

Family and domain databases

InterProiView protein in InterPro
IPR030382 MeTrfase_TRM5/TYW2
IPR029063 SAM-dependent_MTases
IPR026274 tRNA_wybutosine_synth_prot_2
PfamiView protein in Pfam
PF02475 Met_10, 1 hit
PIRSFiPIRSF038972 Trm12, 1 hit
SUPFAMiSSF53335 SSF53335, 2 hits
PROSITEiView protein in PROSITE
PS51684 SAM_MT_TRM5_TYW2, 1 hit

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

Similar proteinsi

Entry informationi

Entry nameiTYW2_YEAST
AccessioniPrimary (citable) accession number: Q04235
Secondary accession number(s): D6VZH0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: May 23, 2018
This is version 133 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

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

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