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UniProtKB - P0ABT5 (DUSB_ECOLI)

Entry version 109 (02 Dec 2020)
Sequence version 1 (25 Oct 2005)
Previous versions | rss
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Protein

tRNA-dihydrouridine synthase B

Gene

dusB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score:

Annotation score:4 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 synthesis of 5,6-dihydrouridine (D), a modified base found in the D-loop of most tRNAs, via the reduction of the C5-C6 double bond in target uridines.UniRule annotation1 Publication

Miscellaneous

DusB and DusC together account for about half of the 5,6-dihydrouridine modification observed in wild-type cellular tRNA, and DusA accounts for the other half. These three enzymes seem to act site-specifically on the tRNA D-loop and contain nonredundant catalytic functions in vivo.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

<p>This subsection of the 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

FMNUniRule annotationBy similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">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 sitei70FMNUniRule annotationBy similarity1
<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 sitei100Proton donorUniRule annotationBy similarity1
Binding sitei139FMNUniRule annotationBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes a region in the protein which binds nucleotide phosphates. It always involves more than one amino acid and includes all residues involved in nucleotide-binding.<p><a href='/help/np_bind' target='_top'>More...</a></p>Nucleotide bindingi16 – 18FMNUniRule annotationBy similarity3
Nucleotide bindingi200 – 202FMNUniRule annotationBy similarity3
Nucleotide bindingi224 – 225FMNUniRule annotationBy similarity2

<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

Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<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, RNA-binding, tRNA-binding
Biological processtRNA processing
LigandFlavoprotein, FMN, NADP

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		EcoCyc:EG11311-MONOMER
MetaCyc:EG11311-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-dihydrouridine synthase B1 PublicationUniRule annotation (EC:1.3.1.-UniRule annotationCurated)
<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:dusB1 PublicationUniRule annotation
Synonyms:yhdG
Ordered Locus Names:b3260, JW3228
<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 lineageiBacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia ›
<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

A dusA dusB dusC triple mutant exhibits a complete lack of 5,6-dihydrouridine modification in cellular tRNA, whereas each single mutant exhibits a partial reduction, compared to wild type.1 Publication

<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_00001620841 – 321tRNA-dihydrouridine synthase BAdd BLAST321

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...jPOSTi		P0ABT5

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

More...PaxDbi		P0ABT5

PRoteomics IDEntifications database

More...PRIDEi		P0ABT5

<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		4261865, 16 interactors

Database of interacting proteins

More...DIPi		DIP-48240N

Protein interaction database and analysis system

More...IntActi		P0ABT5, 4 interactors

STRING: functional protein association networks

More...STRINGi		511145.b3260

<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

1321
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		P0ABT5

Database of comparative protein structure models

More...ModBasei		Search...

Protein Data Bank in Europe - Knowledge Base

More...PDBe-KBi		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

<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 Dus family. DusB subfamily.UniRule annotationCurated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		COG0042, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_013299_0_1_6

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P0ABT5

Database for complete collections of gene phylogenies

More...PhylomeDBi		P0ABT5

Family and domain databases

Conserved Domains Database

More...CDDi		cd02801, DUS_like_FMN, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		1.10.1200.80, 1 hit
3.20.20.70, 1 hit

HAMAP database of protein families

More...HAMAPi		MF_02042, DusB_subfam, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR013785, Aldolase_TIM
IPR035587, DUS-like_FMN-bd
IPR032887, DusB
IPR024036, tRNA-dHydroUridine_Synthase_C
IPR004652, tRNA_dU_NifR3
IPR001269, tRNA_hU_synthase
IPR018517, tRNA_hU_synthase_CS

Pfam protein domain database

More...Pfami		View protein in Pfam
PF01207, Dus, 1 hit

PIRSF; a whole-protein classification database

More...PIRSFi		PIRSF006621, Dus, 1 hit

TIGRFAMs; a protein family database

More...TIGRFAMsi		TIGR00737, nifR3_yhdG, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS01136, UPF0034, 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.

P0ABT5-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MRIGQYQLRN RLIAAPMAGI TDRPFRTLCY EMGAGLTVSE MMSSNPQVWE 
        60         70         80         90        100
SDKSRLRMVH IDEPGIRTVQ IAGSDPKEMA DAARINVESG AQIIDINMGC 
       110        120        130        140        150
PAKKVNRKLA GSALLQYPDV VKSILTEVVN AVDVPVTLKI RTGWAPEHRN 
       160        170        180        190        200
CEEIAQLAED CGIQALTIHG RTRACLFNGE AEYDSIRAVK QKVSIPVIAN 
       210        220        230        240        250
GDITDPLKAR AVLDYTGADA LMIGRAAQGR PWIFREIQHY LDTGELLPPL 
       260        270        280        290        300
PLAEVKRLLC AHVRELHDFY GPAKGYRIAR KHVSWYLQEH APNDQFRRTF 
       310        320 
NAIEDASEQL EALEAYFENF A
Length:321
Mass (Da):35,866
Last modified:October 25, 2005 - 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:iB9A31AB459825DE5
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 conflicti131A → R in CAA44270 (PubMed:1547773).Curated1
Sequence conflicti267H → D in CAA44270 (PubMed:1547773).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
X62399 Genomic DNA Translation: CAA44270.1
M95784 Genomic DNA Translation: AAA23782.1
U18997 Genomic DNA Translation: AAA58064.1
U00096 Genomic DNA Translation: AAC76292.1
AP009048 Genomic DNA Translation: BAE77301.1
S67010 Genomic DNA Translation: AAB28770.2
J03816 Genomic DNA No translation available.
J03245 Genomic DNA Translation: AAA83855.1

Protein sequence database of the Protein Information Resource

More...PIRi		B47043

NCBI Reference Sequences

More...RefSeqi		NP_417726.1, NC_000913.3
WP_001219652.1, NZ_STEB01000012.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAC76292; AAC76292; b3260
BAE77301; BAE77301; BAE77301

Database of genes from NCBI RefSeq genomes

More...GeneIDi		52075159
947707

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ecj:JW3228
eco:b3260

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|1411691.4.peg.3468

<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
X62399 Genomic DNA Translation: CAA44270.1
M95784 Genomic DNA Translation: AAA23782.1
U18997 Genomic DNA Translation: AAA58064.1
U00096 Genomic DNA Translation: AAC76292.1
AP009048 Genomic DNA Translation: BAE77301.1
S67010 Genomic DNA Translation: AAB28770.2
J03816 Genomic DNA No translation available.
J03245 Genomic DNA Translation: AAA83855.1
PIRiB47043
RefSeqiNP_417726.1, NC_000913.3
WP_001219652.1, NZ_STEB01000012.1

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
6EI9X-ray2.55A/B1-321[»]
SMRiP0ABT5
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGRIDi4261865, 16 interactors
DIPiDIP-48240N
IntActiP0ABT5, 4 interactors
STRINGi511145.b3260

Proteomic databases

jPOSTiP0ABT5
PaxDbiP0ABT5
PRIDEiP0ABT5

Genome annotation databases

EnsemblBacteriaiAAC76292; AAC76292; b3260
BAE77301; BAE77301; BAE77301
GeneIDi52075159
947707
KEGGiecj:JW3228
eco:b3260
PATRICifig|1411691.4.peg.3468

Organism-specific databases

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

More...EchoBASEi		EB1287

Phylogenomic databases

eggNOGiCOG0042, Bacteria
HOGENOMiCLU_013299_0_1_6
InParanoidiP0ABT5
PhylomeDBiP0ABT5

Enzyme and pathway databases

BioCyciEcoCyc:EG11311-MONOMER
MetaCyc:EG11311-MONOMER

Miscellaneous databases

Protein Ontology

More...PROi		PR:P0ABT5

Family and domain databases

CDDicd02801, DUS_like_FMN, 1 hit
Gene3Di1.10.1200.80, 1 hit
3.20.20.70, 1 hit
HAMAPiMF_02042, DusB_subfam, 1 hit
InterProiView protein in InterPro
IPR013785, Aldolase_TIM
IPR035587, DUS-like_FMN-bd
IPR032887, DusB
IPR024036, tRNA-dHydroUridine_Synthase_C
IPR004652, tRNA_dU_NifR3
IPR001269, tRNA_hU_synthase
IPR018517, tRNA_hU_synthase_CS
PfamiView protein in Pfam
PF01207, Dus, 1 hit
PIRSFiPIRSF006621, Dus, 1 hit
TIGRFAMsiTIGR00737, nifR3_yhdG, 1 hit
PROSITEiView protein in PROSITE
PS01136, UPF0034, 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 nameiDUSB_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: P0ABT5
Secondary accession number(s): P25717, Q2M8V5
<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: October 25, 2005
Last sequence update: October 25, 2005
Last modified: December 2, 2020
This is version 109 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, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
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