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Entry version 157 (13 Nov 2019)
Sequence version 1 (01 Aug 1991)
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Protein

tRNA/tmRNA (uracil-C(5))-methyltransferase

Gene

trmA

Organism
Escherichia coli (strain K12)
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

Dual-specificity methyltransferase that catalyzes the formation of 5-methyluridine at position 54 (m5U54) in all tRNAs, and that of position 341 (m5U341) in tmRNA (transfer-mRNA).UniRule annotation3 Publications

<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 sitei190S-adenosyl-L-methionineUniRule annotation1
Binding sitei218S-adenosyl-L-methionine; via carbonyl oxygenUniRule annotation1
Binding sitei223S-adenosyl-L-methionineUniRule annotation1
Binding sitei239S-adenosyl-L-methionineUniRule annotation1
Binding sitei299S-adenosyl-L-methionineUniRule 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 sitei324NucleophileUniRule annotation1 Publication1
Active sitei358Proton acceptorUniRule annotation1 Publication1

<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

  • rRNA binding Source: EcoCyc
  • S-adenosylmethionine-dependent tRNA (m5U54) methyltransferase activity Source: EcoCyc
  • tRNA binding Source: EcoCyc

GO - Biological processi

  • tRNA methylation Source: EcoCyc

<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

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
EcoCyc:EG11022-MONOMER
ECOL316407:JW3937-MONOMER
MetaCyc:EG11022-MONOMER

BRENDA Comprehensive Enzyme Information System

More...
BRENDAi
2.1.1.35 2026

<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/tmRNA (uracil-C(5))-methyltransferaseUniRule annotation (EC:2.1.1.-UniRule annotation, EC:2.1.1.35UniRule annotation)
Alternative name(s):
tRNA (uracil(54)-C(5))-methyltransferaseUniRule annotation
tRNA(m5U54)-methyltransferaseUniRule annotation
Short name:
RUMTUniRule annotation
tmRNA (uracil(341)-C(5))-methyltransferaseUniRule annotation
<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:trmAUniRule annotation
Ordered Locus Names:b3965, JW3937
<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>OrganismiEscherichia coli (strain K12)
<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 identifieri83333 [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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
<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
  • UP000000318 <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
  • UP000000625 Componenti: Chromosome

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

GO - Cellular componenti

<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

<p>This subsection of the ‘Pathology and Biotech’ section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

Cells lacking this gene exhibit a lack of m5U modification in tmRNA.1 Publication

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>Mutagenesisi358E → Q: Loss of catalytic activity. 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.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001618591 – 366tRNA/tmRNA (uracil-C(5))-methyltransferaseAdd BLAST366

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...
jPOSTi
P23003

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

More...
PaxDbi
P23003

PRoteomics IDEntifications database

More...
PRIDEi
P23003

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

<p>This subsection of the ‘Expression’ section reports the experimentally proven effects of inducers and repressors (usually chemical compounds or environmental factors) on the level of protein (or mRNA) expression (up-regulation, down-regulation, constitutive expression).<p><a href='/help/induction' target='_top'>More...</a></p>Inductioni

Growth rate-dependent regulation of transcription. Is a novel example of a mRNA regulated through a mechanism similar to that of a stable RNA (rRNA).

<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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections (‘Function’, ‘PTM / Processing’, ‘Pathology and Biotech’) according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei190Interaction with RNA1
Sitei299Interaction with RNA1
Sitei302Interaction with RNA1

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...
BioGridi
4260659, 1 interactor

Database of interacting proteins

More...
DIPi
DIP-11031N

Protein interaction database and analysis system

More...
IntActi
P23003, 5 interactors

STRING: functional protein association networks

More...
STRINGi
511145.b3965

<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

Secondary structure

1366
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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

More...
SMRi
P23003

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...
EvolutionaryTracei
P23003

<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

<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

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4107R9T Bacteria
COG2265 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000218626

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P23003

KEGG Orthology (KO)

More...
KOi
K00557

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P23003

Family and domain databases

HAMAP database of protein families

More...
HAMAPi
MF_01011 RNA_methyltr_TrmA, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR030390 MeTrfase_TrmA_AS
IPR030391 MeTrfase_TrmA_CS
IPR029063 SAM-dependent_MTases
IPR011869 TrmA_MeTrfase
IPR010280 U5_MeTrfase_fam

The PANTHER Classification System

More...
PANTHERi
PTHR47790 PTHR47790, 1 hit

Pfam protein domain database

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

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF53335 SSF53335, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR02143 trmA_only, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS51687 SAM_MT_RNA_M5U, 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.

P23003-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MTPEHLPTEQ YEAQLAEKVV RLQSMMAPFS DLVPEVFRSP VSHYRMRAEF
60 70 80 90 100
RIWHDGDDLY HIIFDQQTKS RIRVDSFPAA SELINQLMTA MIAGVRNNPV
110 120 130 140 150
LRHKLFQIDY LTTLSNQAVV SLLYHKKLDD EWRQEAEALR DALRAQNLNV
160 170 180 190 200
HLIGRATKTK IELDQDYIDE RLPVAGKEMI YRQVENSFTQ PNAAMNIQML
210 220 230 240 250
EWALDVTKGS KGDLLELYCG NGNFSLALAR NFDRVLATEI AKPSVAAAQY
260 270 280 290 300
NIAANHIDNV QIIRMAAEEF TQAMNGVREF NRLQGIDLKS YQCETIFVDP
310 320 330 340 350
PRSGLDSETE KMVQAYPRIL YISCNPETLC KNLETLSQTH KVERLALFDQ
360
FPYTHHMECG VLLTAK
Length:366
Mass (Da):41,967
Last modified:August 1, 1991 - v1
<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:iA7A65FD98380D27D
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
M57568 Genomic DNA Translation: AAA24691.1
U00006 Genomic DNA Translation: AAC43071.1
U00096 Genomic DNA Translation: AAC76947.1
AP009048 Genomic DNA Translation: BAE77346.1
X66026 Genomic DNA Translation: CAA46825.1

Protein sequence database of the Protein Information Resource

More...
PIRi
A37321

NCBI Reference Sequences

More...
RefSeqi
NP_418400.1, NC_000913.3
WP_000187022.1, NZ_STEB01000037.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAC76947; AAC76947; b3965
BAE77346; BAE77346; BAE77346

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
947143

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ecj:JW3937
eco:b3965

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|1411691.4.peg.2739

<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
M57568 Genomic DNA Translation: AAA24691.1
U00006 Genomic DNA Translation: AAC43071.1
U00096 Genomic DNA Translation: AAC76947.1
AP009048 Genomic DNA Translation: BAE77346.1
X66026 Genomic DNA Translation: CAA46825.1
PIRiA37321
RefSeqiNP_418400.1, NC_000913.3
WP_000187022.1, NZ_STEB01000037.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3BT7X-ray2.43A/B1-366[»]
SMRiP23003
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGridi4260659, 1 interactor
DIPiDIP-11031N
IntActiP23003, 5 interactors
STRINGi511145.b3965

Proteomic databases

jPOSTiP23003
PaxDbiP23003
PRIDEiP23003

Genome annotation databases

EnsemblBacteriaiAAC76947; AAC76947; b3965
BAE77346; BAE77346; BAE77346
GeneIDi947143
KEGGiecj:JW3937
eco:b3965
PATRICifig|1411691.4.peg.2739

Organism-specific databases

EchoBASE - an integrated post-genomic database for E. coli

More...
EchoBASEi
EB1015

Phylogenomic databases

eggNOGiENOG4107R9T Bacteria
COG2265 LUCA
HOGENOMiHOG000218626
InParanoidiP23003
KOiK00557
PhylomeDBiP23003

Enzyme and pathway databases

BioCyciEcoCyc:EG11022-MONOMER
ECOL316407:JW3937-MONOMER
MetaCyc:EG11022-MONOMER
BRENDAi2.1.1.35 2026

Miscellaneous databases

EvolutionaryTraceiP23003

Protein Ontology

More...
PROi
PR:P23003

Family and domain databases

HAMAPiMF_01011 RNA_methyltr_TrmA, 1 hit
InterProiView protein in InterPro
IPR030390 MeTrfase_TrmA_AS
IPR030391 MeTrfase_TrmA_CS
IPR029063 SAM-dependent_MTases
IPR011869 TrmA_MeTrfase
IPR010280 U5_MeTrfase_fam
PANTHERiPTHR47790 PTHR47790, 1 hit
PfamiView protein in Pfam
PF05958 tRNA_U5-meth_tr, 1 hit
SUPFAMiSSF53335 SSF53335, 1 hit
TIGRFAMsiTIGR02143 trmA_only, 1 hit
PROSITEiView protein in PROSITE
PS51687 SAM_MT_RNA_M5U, 1 hit
PS01230 TRMA_1, 1 hit
PS01231 TRMA_2, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

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 nameiTRMA_ECOLI
<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: P23003
Secondary accession number(s): Q2M8R0
<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: August 1, 1991
Last sequence update: August 1, 1991
Last modified: November 13, 2019
This is version 157 of the entry and version 1 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 programProkaryotic 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

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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