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Entry version 176 (29 Sep 2021)
Sequence version 2 (25 Jul 2006)
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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

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>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

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

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>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
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei591NucleophilePROSITE-ProRule annotation1
Active sitei631Proton acceptorPROSITE-ProRule annotation1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionMethyltransferase, Transferase
Biological processtRNA processing
LigandS-adenosyl-L-methionine

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>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
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:TRM2
Synonyms:NUC2, NUD1, RNC1
Ordered Locus Names:YKR056W
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri559292 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000002311 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome XI

Organism-specific databases

Saccharomyces Genome Database

More...
SGDi
S000001764, TRM2

Eukaryotic Pathogen, Vector and Host Database Resources

More...
VEuPathDBi
FungiDB:YKR056W

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology_and_biotech_section">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi498G → D: Unable to methylate tRNA. 1 Publication1
Mutagenesisi591C → A: Unable to methylate tRNA. 1 Publication1

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001620591 – 639tRNA (uracil(54)-C(5))-methyltransferaseAdd BLAST639

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei92PhosphoserineCombined sources1
Modified residuei93PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQB - The MaxQuant DataBase

More...
MaxQBi
P33753

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
P33753

PRoteomics IDEntifications database

More...
PRIDEi
P33753

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...
iPTMneti
P33753

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...
BioGRIDi
34187, 106 interactors

Molecular INTeraction database

More...
MINTi
P33753

STRING: functional protein association networks

More...
STRINGi
4932.YKR056W

Miscellaneous databases

RNAct, Protein-RNA interaction predictions for model organisms.

More...
RNActi
P33753, protein

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
P33753

Database of comparative protein structure models

More...
ModBasei
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini163 – 228TRAMPROSITE-ProRule annotationAdd BLAST66

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni78 – 113DisorderedSequence analysisAdd BLAST36

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes the position of regions of compositional bias within the protein and the particular type of amino acids that are over-represented within those regions.<p><a href='/help/compbias' target='_top'>More...</a></p>Compositional biasi78 – 99Polar residuesSequence analysisAdd BLAST22

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

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

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG2187, Eukaryota

Ensembl GeneTree

More...
GeneTreei
ENSGT00530000063723

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_014689_3_2_1

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P33753

Identification of Orthologs from Complete Genome Data

More...
OMAi
FYAGDMK

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR030390, 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

The PANTHER Classification System

More...
PANTHERi
PTHR11061, PTHR11061, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF01938, TRAM, 1 hit
PF05958, tRNA_U5-meth_tr, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF50249, SSF50249, 1 hit
SSF53335, SSF53335, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS51687, SAM_MT_RNA_M5U, 1 hit
PS50926, TRAM, 1 hit
PS01230, TRMA_1, 1 hit
PS01231, TRMA_2, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>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
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iE7EC5B1378F7C361
GO

<p>This subsection of the 'Sequence' section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>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.Curated
The sequence CAA82134 differs from that shown. Reason: Frameshift.Curated
The sequence CAC01942 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Sequence' section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti24H → Y in CAA78500 (PubMed:1408836).Curated1

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
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

Protein sequence database of the Protein Information Resource

More...
PIRi
S37744

NCBI Reference Sequences

More...
RefSeqi
NP_012982.2, NM_001179846.1

Genome annotation databases

Ensembl fungal genome annotation project

More...
EnsemblFungii
YKR056W_mRNA; YKR056W; YKR056W

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
853930

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
sce:YKR056W

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>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

SMRiP33753
ModBaseiSearch...

Protein-protein interaction databases

BioGRIDi34187, 106 interactors
MINTiP33753
STRINGi4932.YKR056W

PTM databases

iPTMnetiP33753

Proteomic databases

MaxQBiP33753
PaxDbiP33753
PRIDEiP33753

Genome annotation databases

EnsemblFungiiYKR056W_mRNA; YKR056W; YKR056W
GeneIDi853930
KEGGisce:YKR056W

Organism-specific databases

SGDiS000001764, TRM2
VEuPathDBiFungiDB:YKR056W

Phylogenomic databases

eggNOGiKOG2187, Eukaryota
GeneTreeiENSGT00530000063723
HOGENOMiCLU_014689_3_2_1
InParanoidiP33753
OMAiFYAGDMK

Miscellaneous databases

Protein Ontology

More...
PROi
PR:P33753
RNActiP33753, protein

Family and domain databases

InterProiView protein in InterPro
IPR030390, 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
PANTHERiPTHR11061, PTHR11061, 1 hit
PfamiView protein in Pfam
PF01938, TRAM, 1 hit
PF05958, tRNA_U5-meth_tr, 1 hit
SUPFAMiSSF50249, SSF50249, 1 hit
SSF53335, SSF53335, 1 hit
PROSITEiView protein in PROSITE
PS51687, SAM_MT_RNA_M5U, 1 hit
PS50926, TRAM, 1 hit
PS01230, TRMA_1, 1 hit
PS01231, TRMA_2, 1 hit

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiTRM2_YEAST
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P33753
Secondary accession number(s): D6VXB7
, P30618, Q86ZR6, Q9HGQ5
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: July 25, 2006
Last modified: September 29, 2021
This is version 176 of the entry and version 2 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Reference proteome

Documents

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