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Protein

tRNA (uracil(54)-C(5))-methyltransferase

Gene

TRM2

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

Catalyzes the formation of 5-methyl-uridine at position 54 (m5U54) in all tRNA. May also have a role in tRNA stabilization or maturation.2 Publications

Catalytic activityi

S-adenosyl-L-methionine + uracil(54) in tRNA = S-adenosyl-L-homocysteine + 5-methyluracil(54) in tRNA.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei461S-adenosyl-L-methioninePROSITE-ProRule annotation1
Binding sitei496S-adenosyl-L-methionine; via carbonyl oxygenPROSITE-ProRule annotation1
Binding sitei517S-adenosyl-L-methioninePROSITE-ProRule annotation1
Binding sitei564S-adenosyl-L-methioninePROSITE-ProRule annotation1
Active sitei591NucleophilePROSITE-ProRule annotation1
Active sitei631Proton acceptorPROSITE-ProRule annotation1

GO - Molecular functioni

GO - Biological processi

  • DNA repair Source: SGD
  • double-strand break repair Source: SGD
  • tRNA modification 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

BioCyciYEAST:G3O-32025-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA (uracil(54)-C(5))-methyltransferase (EC:2.1.1.35)
Alternative name(s):
Transfer RNA methyltransferase 2
tRNA(m5U54)-methyltransferase
Gene namesi
Name:TRM2
Synonyms:NUC2, NUD1, RNC1
Ordered Locus Names:YKR056W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XI

Organism-specific databases

EuPathDBiFungiDB:YKR056W.
SGDiS000001764. TRM2.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi498G → D: Unable to methylate tRNA. 1 Publication1
Mutagenesisi591C → A: Unable to methylate tRNA. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001620591 – 639tRNA (uracil(54)-C(5))-methyltransferaseAdd BLAST639

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei92PhosphoserineCombined sources1
Modified residuei93PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP33753.
PRIDEiP33753.

PTM databases

iPTMnetiP33753.

Interactioni

Protein-protein interaction databases

BioGridi34187. 34 interactors.
MINTiMINT-2781813.

Structurei

3D structure databases

ProteinModelPortaliP33753.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini163 – 228TRAMPROSITE-ProRule annotationAdd BLAST66

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi5 – 12Poly-Phe8

Sequence similaritiesi

Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family.PROSITE-ProRule annotation
Contains 1 TRAM domain.PROSITE-ProRule annotation

Phylogenomic databases

GeneTreeiENSGT00530000063723.
HOGENOMiHOG000029869.
InParanoidiP33753.
KOiK15331.
OMAiQPRINEI.
OrthoDBiEOG092C156C.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR030390. MeTrfase_TrmA_AS.
IPR030391. MeTrfase_TrmA_CS.
IPR012340. NA-bd_OB-fold.
IPR029063. SAM-dependent_MTases.
IPR002792. TRAM_dom.
IPR025795. tRNA_(uracil-5-)_MeTrfase.
IPR010280. U5_MeTrfase_fam.
[Graphical view]
PfamiPF01938. TRAM. 1 hit.
PF05958. tRNA_U5-meth_tr. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
SSF53335. SSF53335. 1 hit.
PROSITEiPS51687. SAM_MT_RNA_M5U. 1 hit.
PS50926. TRAM. 1 hit.
PS01230. TRMA_1. 1 hit.
PS01231. TRMA_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P33753-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MYEQFEFSFF FFENSDNKVK YKAHLISSIK RWSIITCMRC FWTVQKSIFK
60 70 80 90 100
ARFFACRNFV KKHNYKLIST MTGSTEMVPP TMKHTVDNKR LSSPLTDSGN
110 120 130 140 150
RRTKKPKLRK YKAKKVETTS PMGVLEFEVN DLLKSQNLSR EQVLNDVTSI
160 170 180 190 200
LNDKSSTDGP IVLQYHREVK NVKVLEITSN GNGLALIDNP VETEKKQVVI
210 220 230 240 250
IPFGLPGDVV NIKVFKTHPY YVESDLLDVV EKSPMRRDDL IRDKYFGKSS
260 270 280 290 300
GSQLEFLTYD DQLELKRKTI MNAYKFFAPR LVAEKLLPPF DTTVASPLQF
310 320 330 340 350
GYRTKITPHF DMPKRKQKEL SVRPPLGFGQ KGRPQWRKDT LDIGGHGSIL
360 370 380 390 400
DIDECVLATE VLNKGLTNER RKFEQEFKNY KKGATILLRE NTTILDPSKP
410 420 430 440 450
TLEQLTEEAS RDENGDISYV EVEDKKNNVR LAKTCVTNPR QIVTEYVDGY
460 470 480 490 500
TFNFSAGEFF QNNNSILPIV TKYVRDNLQA PAKGDDNKTK FLVDAYCGSG
510 520 530 540 550
LFSICSSKGV DKVIGVEISA DSVSFAEKNA KANGVENCRF IVGKAEKLFE
560 570 580 590 600
SIDTPSENTS VILDPPRKGC DELFLKQLAA YNPAKIIYIS CNVHSQARDV
610 620 630
EYFLKETENG SAHQIESIRG FDFFPQTHHV ESVCIMKRI
Length:639
Mass (Da):72,852
Last modified:July 25, 2006 - v2
Checksum:iE7EC5B1378F7C361
GO

Sequence cautioni

The sequence CAA78500 differs from that shown. Cloning artifact which fused this protein with RHO4.Curated
The sequence CAA81021 differs from that shown. Reason: Frameshift at position 582.Curated
The sequence CAA82134 differs from that shown. Reason: Frameshift at position 582.Curated
The sequence CAC01942 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti24H → Y in CAA78500 (PubMed:1408836).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z25734 Genomic DNA. Translation: CAA81021.1. Frameshift.
AJ250970 Genomic DNA. Translation: CAC01942.1. Different initiation.
Z28281 Genomic DNA. Translation: CAA82134.1. Frameshift.
Z14126 Genomic DNA. Translation: CAA78500.1. Sequence problems.
AY260897 Genomic DNA. Translation: AAP21765.1.
BK006944 Genomic DNA. Translation: DAA09207.1.
PIRiS37744.
RefSeqiNP_012982.2. NM_001179846.1.

Genome annotation databases

EnsemblFungiiYKR056W; YKR056W; YKR056W.
GeneIDi853930.
KEGGisce:YKR056W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z25734 Genomic DNA. Translation: CAA81021.1. Frameshift.
AJ250970 Genomic DNA. Translation: CAC01942.1. Different initiation.
Z28281 Genomic DNA. Translation: CAA82134.1. Frameshift.
Z14126 Genomic DNA. Translation: CAA78500.1. Sequence problems.
AY260897 Genomic DNA. Translation: AAP21765.1.
BK006944 Genomic DNA. Translation: DAA09207.1.
PIRiS37744.
RefSeqiNP_012982.2. NM_001179846.1.

3D structure databases

ProteinModelPortaliP33753.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34187. 34 interactors.
MINTiMINT-2781813.

PTM databases

iPTMnetiP33753.

Proteomic databases

MaxQBiP33753.
PRIDEiP33753.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYKR056W; YKR056W; YKR056W.
GeneIDi853930.
KEGGisce:YKR056W.

Organism-specific databases

EuPathDBiFungiDB:YKR056W.
SGDiS000001764. TRM2.

Phylogenomic databases

GeneTreeiENSGT00530000063723.
HOGENOMiHOG000029869.
InParanoidiP33753.
KOiK15331.
OMAiQPRINEI.
OrthoDBiEOG092C156C.

Enzyme and pathway databases

BioCyciYEAST:G3O-32025-MONOMER.

Miscellaneous databases

PROiP33753.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR030390. MeTrfase_TrmA_AS.
IPR030391. MeTrfase_TrmA_CS.
IPR012340. NA-bd_OB-fold.
IPR029063. SAM-dependent_MTases.
IPR002792. TRAM_dom.
IPR025795. tRNA_(uracil-5-)_MeTrfase.
IPR010280. U5_MeTrfase_fam.
[Graphical view]
PfamiPF01938. TRAM. 1 hit.
PF05958. tRNA_U5-meth_tr. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
SSF53335. SSF53335. 1 hit.
PROSITEiPS51687. SAM_MT_RNA_M5U. 1 hit.
PS50926. TRAM. 1 hit.
PS01230. TRMA_1. 1 hit.
PS01231. TRMA_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiTRM2_YEAST
AccessioniPrimary (citable) accession number: P33753
Secondary accession number(s): D6VXB7
, P30618, Q86ZR6, Q9HGQ5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: July 25, 2006
Last modified: November 2, 2016
This is version 145 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Caution

Was originally thought to be an endo-exonuclease.1 Publication
It is uncertain whether Met-1, Met-38, Met-71, Met-77 or Met-82 is the initiator.Curated

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

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