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Entry version 31 (11 Dec 2019)
Sequence version 1 (27 Jul 2011)
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Protein

Thymine dioxygenase JBP1

Gene

JBP1

Organism
Trypanosoma brucei brucei (strain 927/4 GUTat10.1)
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

Dioxygenase that catalyzes the first step of DNA base J (beta-d-glucosyl-HOMedU) biosynthesis by converting thymine to 5-hydroxymethyluracil (HOMedU). DNA base J is a hypermodified thymidine residue found in the genome of kinetoplastid parasites, which is localized primarily to repetitive DNA, namely the telomeres, and is implicated in the regulation of antigenic variation. Also specifically binds to base J-containing DNA (J-DNA). Involved in propagation and maintenance of DNA base J synthesis initiated by JBP2 by specifically binding already synthesized DNA base J and propagating J synthesis. Thymine dioxygenase activity and J-DNA-binding are independent functions.2 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

<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

Fe2+By similarityNote: Binds 1 Fe2+ ion per subunit.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the ‘Description’ field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi213Iron; catalytic1 Publication1
Metal bindingi215Iron; catalytic1 Publication1
Metal bindingi263Iron; catalyticBy similarity1
<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 sitei2792-oxoglutarateBy similarity1
<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>Sitei548Involved in J base recognition, conferring specificity towards J-DNABy similarity1

<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

  • DNA binding Source: GeneDB
  • ferrous iron binding Source: GeneDB
  • thymine dioxygenase activity Source: GeneDB

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 functionDioxygenase, DNA-binding, Oxidoreductase
LigandIron, Metal-binding

<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:
Thymine dioxygenase JBP1 (EC:1.14.11.62 Publications)
Alternative name(s):
J-binding protein 1
Thymidine hydroxylase JBP1
<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:JBP1
ORF Names:Tb11.01.5220
<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>OrganismiTrypanosoma brucei brucei (strain 927/4 GUTat10.1)
<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 identifieri185431 [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 lineageiEukaryotaEuglenozoaKinetoplastidaTrypanosomatidaeTrypanosoma
<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
  • UP000008524 <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 11 Scaffold 1

Organism-specific databases

Eukaryotic Pathogen Database Resources

More...
EuPathDBi
TriTrypDB:Tb927.11.13640

<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

Keywords - Cellular componenti

Nucleus

<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

Does not affect growth, gene expression or the stability of some repetitive DNA sequences. The genome contains only about 5% of the wild-type level of J in their DNA. Cells lacking both JBP1 and JBP2 show a complete absence of base J.2 Publications

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>Mutagenesisi213H → S: Impairs DNA base J biosynthesis. 1 Publication1
Mutagenesisi215D → S: Impairs DNA base J biosynthesis. 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_00003775551 – 839Thymine dioxygenase JBP1Add BLAST839

Proteomic databases

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

More...
PaxDbi
P86938

PRoteomics IDEntifications database

More...
PRIDEi
P86938

<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 provides information on the expression of the gene product at various stages of a cell, tissue or organism development. By default, the information is derived from experiments at the mRNA level, unless specified ‘at the protein level’.<p><a href='/help/developmental_stage' target='_top'>More...</a></p>Developmental stagei

Expressed in bloodstream form and significantly less in procyclic form.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_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Monomer. Binds to DNA as a monomer (By similarity).

By similarity

<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
P86938

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

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>Regioni86 – 288Thymine dioxygenaseBy similarityAdd BLAST203
Regioni415 – 583DNA-binding JBP1 domainBy similarityAdd BLAST169

<p>This subsection of the ‘Family and domains’ section provides general information on the biological role of a domain. The term ‘domain’ is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

The DNA-binding JBP1 domain (DB-JBP1) is necessary and sufficient for binding to J-DNA.By similarity

<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 TET family. JBP1 subfamily.Curated

Phylogenomic databases

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000113125

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P86938

KEGG Orthology (KO)

More...
KOi
K22406

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
1.20.120.1440, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR024779 2OGFeDO_noxygenase_dom
IPR041241 DB_JBP1
IPR043111 DB_JBP1_sf

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF18526 DB_JBP1, 1 hit
PF12851 Tet_JBP, 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.

P86938-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MRRQVKKVLR EKADDSMKPG WDVYQPSNDV VYAFNHYMQG SQIDAEAREK
60 70 80 90 100
AEKAFQEAVK KHPFHNNADH TVDFHGTTVF RNAKGKVCGV LIPKALPSFA
110 120 130 140 150
TSMAADVLEC AVARTSLRSA LFGGVSPNSG IAGYFDYRGT PVELKCRKTS
160 170 180 190 200
FTYEHTKEWR SVFPMIDYTS AIYKAALPDH WKAQDAAVPD VVRIHGSPFS
210 220 230 240 250
TLTVNERFRT ASHTDNGDFD NGYGVLAVLK GEYSGLSLAL DDYGVCFNMQ
260 270 280 290 300
PTDVLLFDTH LFHSNTELEA KEANATWNRL SCVFYYRAAL GEQPCVEEYR
310 320 330 340 350
RRLKKAKEEK STSLSFNHIE QKDNGENTNK PAPVYPVSLT PFSCAASAWA
360 370 380 390 400
LRGCAAAMLT RLHGLVRENA SLMTELFGEP VEVADGLPRR APEEIIPVHK
410 420 430 440 450
HTNVQMHYLG GFSEKGDILN EAMNKRHYLD KENLQKMFGE EFVNIWTQSR
460 470 480 490 500
THWLQLVKKE WEHQKETNPT RTRFSWNNTS AMNFAFFDLC DVAKQLMCGA
510 520 530 540 550
FGDREVNKKE EQSFWGMFAA HLDNACINEI GMLQGSMGMH KLNVKLKDYN
560 570 580 590 600
FGGTRYLKDM PPEEQERRRR RRLEIEQARR RAPICDSESG DWLRNEAFDY
610 620 630 640 650
QTEDVAVNYE REQWITPENN AKRFGFPERG VYGAEGAATG TISVLIVLPK
660 670 680 690 700
PTNHRQKTCE LPTSREADRI MKNPAAQRLL CAKPCNIGLS TSSNKSRTVL
710 720 730 740 750
CGNIRIDKVF DGGSVGGKMY DFVIMRHLLA ATTGEREPLE CLVRWTSLAR
760 770 780 790 800
YCTFVVEVDL LDRHHYILKS EIGEEYSAVS EICFSALYSA TYARDKVNLR
810 820 830
TTPCLLSFID KSGNMLESRF KFNGSPLNTV AFVVRRREK
Length:839
Mass (Da):95,251
Last modified:July 27, 2011 - 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:iB3BEECD851CC0FE7
GO

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
CH464491 Genomic DNA Translation: EAN80308.1

NCBI Reference Sequences

More...
RefSeqi
XP_829420.1, XM_824327.1

Genome annotation databases

GeneDB pathogen genome database from Sanger Institute

More...
GeneDBi
Tb927.11.13640:pep

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
3665128

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
tbr:Tb11.01.5220

<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
CH464491 Genomic DNA Translation: EAN80308.1
RefSeqiXP_829420.1, XM_824327.1

3D structure databases

SMRiP86938
ModBaseiSearch...

Proteomic databases

PaxDbiP86938
PRIDEiP86938

Genome annotation databases

GeneDBiTb927.11.13640:pep
GeneIDi3665128
KEGGitbr:Tb11.01.5220

Organism-specific databases

EuPathDBiTriTrypDB:Tb927.11.13640

Phylogenomic databases

HOGENOMiHOG000113125
InParanoidiP86938
KOiK22406

Family and domain databases

Gene3Di1.20.120.1440, 1 hit
InterProiView protein in InterPro
IPR024779 2OGFeDO_noxygenase_dom
IPR041241 DB_JBP1
IPR043111 DB_JBP1_sf
PfamiView protein in Pfam
PF18526 DB_JBP1, 1 hit
PF12851 Tet_JBP, 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 nameiJBP1_TRYB2
<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: P86938
Secondary accession number(s): Q382H3, Q9U6M3
<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: July 27, 2011
Last sequence update: July 27, 2011
Last modified: December 11, 2019
This is version 31 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)

<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. SIMILARITY comments
    Index of protein domains and families
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