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Entry version 153 (10 Feb 2021)
Sequence version 2 (15 Jul 1998)
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Protein

tRNA uridine(34) hydroxylase

Gene

trhO

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

Catalyzes oxygen-dependent 5-hydroxyuridine (ho5U) modification at position 34 in tRNAs, the first step in 5-carboxymethoxyuridine (cmo5U) biosynthesis (PubMed:31253794). May be part of an alternate pathway, which is able to bypass cmo5U biogenesis in a subset of tRNAs under aerobic conditions (PubMed:31253794).1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">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%5Fsection">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 sitei200Cysteine persulfide intermediateUniRule 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

  • tRNA modification Source: UniProtKB
  • tRNA wobble uridine modification 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 functionOxidoreductase
Biological processtRNA processing

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
EcoCyc:EG11116-MONOMER
MetaCyc:EG11116-MONOMER

<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%5Fand%5Ftaxonomy%5Fsection">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 uridine(34) hydroxylaseCurated (EC:1.14.-.-1 Publication)
Alternative name(s):
ORF39.9
tRNA hydroxylation protein O1 Publication
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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:trhO1 Publication
Synonyms:yceA
Ordered Locus Names:b1055, JW1042
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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%5Fand%5Ftaxonomy%5Fsection">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%5Fand%5Ftaxonomy%5Fsection">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%5Fand%5Ftaxonomy%5Fsection">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%5Fmanual">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 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

Deletion mutant displays only slight reduction of 5-hydroxyuridine (ho5U) modification at position 34 in tRNAs (PubMed:31253794). Cells lacking both trhP and trhO show complete absence of 5-carboxymethoxyuridine (cmo5U) modification in tRNAs; cells display a temperature-sensitive phenotype and decode codons ending in G (GCG and UCG) less efficiently than the wild-type strain (PubMed:31253794).1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology%5Fand%5Fbiotech%5Fsection">'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>Mutagenesisi112K → A: Reduced 5-carboxymethoxyuridine formation. 1 Publication1
Mutagenesisi114R → A: Reduced 5-carboxymethoxyuridine formation. 1 Publication1
Mutagenesisi200C → A: Reduced 5-carboxymethoxyuridine formation. 1 Publication1
Mutagenesisi201T → A: Reduced 5-carboxymethoxyuridine formation. 1 Publication1
Mutagenesisi202G → A: Does not affect 5-carboxymethoxyuridine formation. 1 Publication1
Mutagenesisi203G → A: Reduced 5-carboxymethoxyuridine formation. 1 Publication1
Mutagenesisi205R → A: Reduced 5-carboxymethoxyuridine formation. 1 Publication1
Mutagenesisi206C → A: Does not affect 5-carboxymethoxyuridine formation. 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_00001614701 – 350tRNA uridine(34) hydroxylaseAdd BLAST350

Proteomic databases

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

More...
PaxDbi
P24188

PRoteomics IDEntifications database

More...
PRIDEi
P24188

<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

Is expressed at all temperatures, but accumulation of yceA transcripts decline with raising temperature. Thus, its expression is repressed by heat shock.1 Publication

<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

<p>This subsection of the '<a href="http://www.uniprot.org/help/interaction%5Fsection">Interaction</a>' section provides information about binary protein-protein interactions. The data presented in this section are a quality-filtered subset of binary interactions automatically derived from the <a href="https://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated at every <a href="http://www.uniprot.org/help/synchronization">UniProt release</a>.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...
BioGRIDi
4262843, 125 interactors

Database of interacting proteins

More...
DIPi
DIP-11521N

Protein interaction database and analysis system

More...
IntActi
P24188, 7 interactors

STRING: functional protein association networks

More...
STRINGi
511145.b1055

<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
P24188

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%5Fand%5Fdomains%5Fsection">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>Domaini146 – 240RhodaneseUniRule annotationAdd BLAST95

<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 TrhO family.UniRule annotation

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
COG1054, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_038878_1_1_6

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P24188

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P24188

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.40.250.10, 1 hit

HAMAP database of protein families

More...
HAMAPi
MF_00469, TrhO, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR001763, Rhodanese-like_dom
IPR036873, Rhodanese-like_dom_sf
IPR022111, Rhodanese_C
IPR020936, TrhO
IPR040503, TRHO_N

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00581, Rhodanese, 1 hit
PF12368, Rhodanese_C, 1 hit
PF17773, UPF0176_N, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00450, RHOD, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF52821, SSF52821, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS50206, RHODANESE_3, 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%5Flength">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%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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.

P24188-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MPVLHNRISN DALKAKMLAE SEPRTTISFY KYFHIADPKA TRDALYQLFT
60 70 80 90 100
ALNVFGRVYL AHEGINAQIS VPASNVETFR AQLYAFDPAL EGLRLNIALD
110 120 130 140 150
DDGKSFWVLR MKVRDRIVAD GIDDPHFDAS NVGEYLQAAE VNAMLDDPDA
160 170 180 190 200
LFIDMRNHYE YEVGHFENAL EIPADTFREQ LPKAVEMMQA HKDKKIVMYC
210 220 230 240 250
TGGIRCEKAS AWMKHNGFNK VWHIEGGIIE YARKAREQGL PVRFIGKNFV
260 270 280 290 300
FDERMGERIS DEIIAHCHQC GAPCDSHTNC KNDGCHLLFI QCPVCAEKYK
310 320 330 340 350
GCCSEICCEE SALPPEEQRR RRAGRENGNK IFNKSRGRLN TTLCIPDPTE
Length:350
Mass (Da):39,781
Last modified:July 15, 1998 - 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:i61AB5F317B0C221B
GO

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 conflicti82 – 83QL → HV in CAA43318 (PubMed:1840644).Curated2
Sequence conflicti312A → R in CAA43318 (PubMed:1840644).Curated1

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
X61000 Genomic DNA Translation: CAA43318.1
U00096 Genomic DNA Translation: AAC74139.1
AP009048 Genomic DNA Translation: BAA35853.1

Protein sequence database of the Protein Information Resource

More...
PIRi
D64848

NCBI Reference Sequences

More...
RefSeqi
NP_415573.1, NC_000913.3
WP_001144615.1, NZ_SSZK01000058.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAC74139; AAC74139; b1055
BAA35853; BAA35853; BAA35853

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
57731842
945601

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ecj:JW1042
eco:b1055

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|1411691.4.peg.1214

<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
X61000 Genomic DNA Translation: CAA43318.1
U00096 Genomic DNA Translation: AAC74139.1
AP009048 Genomic DNA Translation: BAA35853.1
PIRiD64848
RefSeqiNP_415573.1, NC_000913.3
WP_001144615.1, NZ_SSZK01000058.1

3D structure databases

SMRiP24188
ModBaseiSearch...

Protein-protein interaction databases

BioGRIDi4262843, 125 interactors
DIPiDIP-11521N
IntActiP24188, 7 interactors
STRINGi511145.b1055

Proteomic databases

PaxDbiP24188
PRIDEiP24188

Genome annotation databases

EnsemblBacteriaiAAC74139; AAC74139; b1055
BAA35853; BAA35853; BAA35853
GeneIDi57731842
945601
KEGGiecj:JW1042
eco:b1055
PATRICifig|1411691.4.peg.1214

Organism-specific databases

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

More...
EchoBASEi
EB1106

Phylogenomic databases

eggNOGiCOG1054, Bacteria
HOGENOMiCLU_038878_1_1_6
InParanoidiP24188
PhylomeDBiP24188

Enzyme and pathway databases

BioCyciEcoCyc:EG11116-MONOMER
MetaCyc:EG11116-MONOMER

Miscellaneous databases

Protein Ontology

More...
PROi
PR:P24188

Family and domain databases

Gene3Di3.40.250.10, 1 hit
HAMAPiMF_00469, TrhO, 1 hit
InterProiView protein in InterPro
IPR001763, Rhodanese-like_dom
IPR036873, Rhodanese-like_dom_sf
IPR022111, Rhodanese_C
IPR020936, TrhO
IPR040503, TRHO_N
PfamiView protein in Pfam
PF00581, Rhodanese, 1 hit
PF12368, Rhodanese_C, 1 hit
PF17773, UPF0176_N, 1 hit
SMARTiView protein in SMART
SM00450, RHOD, 1 hit
SUPFAMiSSF52821, SSF52821, 1 hit
PROSITEiView protein in PROSITE
PS50206, RHODANESE_3, 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 nameiTRHO_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: P24188
Secondary accession number(s): P75924
<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%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 1, 1992
Last sequence update: July 15, 1998
Last modified: February 10, 2021
This is version 153 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 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

Reference proteome

Documents

  1. Uncharacterized protein families (UPF)
    List of uncharacterized protein family (UPF) entries
  2. SIMILARITY comments
    Index of protein domains and families
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