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Protein

Type-4 uracil-DNA glycosylase

Gene

udg

Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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

Removes uracil bases that are present in DNA as a result of either deamination of cytosine or misincorporation of dUMP instead of dTMP. Can remove uracil from double-stranded DNA containing either a U/G, U/A, U/C or U/T base pair as well as from single-stranded DNA (PubMed:12000829, PubMed:14556741). Specifically recognizes uracil that is flipped out from double-stranded DNA (PubMed:14556741).2 Publications

Miscellaneous

The 4Fe-4S cluster may have a structural rather than a catalytic role. Does not appear to be essential for enzyme activity.1 Publication

<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 describes regulatory mechanisms for enzymes, transporters or microbial transcription factors, and reports the components which regulate (by activation or inhibition) the reaction.<p><a href='/help/activity_regulation' target='_top'>More...</a></p>Activity regulationi

Product-inhibited by apurinic/apyrimidinic sites.1 Publication

<p>This subsection of the ‘Function’ section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>Kineticsi

  1. KM=1.0 µM for G/U dsDNA1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘Function’ 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 bindingi13Iron-sulfur (4Fe-4S)Combined sources1 Publication1
    Metal bindingi16Iron-sulfur (4Fe-4S)Combined sources1 Publication1
    <p>This subsection of the ‘Function’ 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 sitei54Uracil; via amide nitrogen1 Publication1
    Binding sitei80Uracil1 Publication1
    Metal bindingi84Iron-sulfur (4Fe-4S)Combined sources1 Publication1
    Metal bindingi100Iron-sulfur (4Fe-4S)Combined sources1 Publication1
    Binding sitei155Uracil1 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

    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 functionHydrolase
    Biological processDNA damage, DNA repair
    Ligand4Fe-4S, Iron, Iron-sulfur, Metal-binding

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    TTHE300852:G1GKC-735-MONOMER

    BRENDA Comprehensive Enzyme Information System

    More...
    BRENDAi
    3.2.2.27 2305

    <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:
    Type-4 uracil-DNA glycosylaseCurated (EC:3.2.2.272 Publications)
    Alternative name(s):
    TTUDGA1 Publication
    TthUDG1 Publication
    <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:udgImported
    Ordered Locus Names:TTHA0718Imported
    <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>OrganismiThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
    <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 identifieri300852 [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 lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus
    <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
    • UP000000532 <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

    <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

    Chemistry databases

    Drug and drug target database

    More...
    DrugBanki
    DB03419 Uracil

    <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_00004391821 – 205Type-4 uracil-DNA glycosylaseAdd BLAST205

    <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.1 Publication

    Protein-protein interaction databases

    STRING: functional protein association networks

    More...
    STRINGi
    300852.TTHA0718

    <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

    1205
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

    Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

    More...
    ProteinModelPortali
    Q5SKC5

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

    More...
    SMRi
    Q5SKC5

    Database of comparative protein structure models

    More...
    ModBasei
    Search...

    MobiDB: a database of protein disorder and mobility annotations

    More...
    MobiDBi
    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>Regioni40 – 42Uracil binding1 Publication3

    <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
    ENOG4108UN4 Bacteria
    COG1573 LUCA

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...
    HOGENOMi
    HOG000196501

    KEGG Orthology (KO)

    More...
    KOi
    K21929

    Identification of Orthologs from Complete Genome Data

    More...
    OMAi
    WLMWQDI

    Database for complete collections of gene phylogenies

    More...
    PhylomeDBi
    Q5SKC5

    Family and domain databases

    Conserved Domains Database

    More...
    CDDi
    cd10030 UDG_F4_TTUDGA_like, 1 hit

    Gene3D Structural and Functional Annotation of Protein Families

    More...
    Gene3Di
    3.40.470.10, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR005273 Ura-DNA_glyco_family4
    IPR005122 Uracil-DNA_glycosylase-like
    IPR036895 Uracil-DNA_glycosylase-like_sf

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF03167 UDG, 1 hit

    Simple Modular Architecture Research Tool; a protein domain database

    More...
    SMARTi
    View protein in SMART
    SM00986 UDG, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF52141 SSF52141, 1 hit

    TIGRFAMs; a protein family database

    More...
    TIGRFAMsi
    TIGR00758 UDG_fam4, 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>.<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.

    Q5SKC5-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MTLELLQAQA QNCTACRLME GRTRVVFGEG NPDAKLMIVG EGPGEEEDKT
    60 70 80 90 100
    GRPFVGKAGQ LLNRILEAAG IPREEVYITN IVKCRPPQNR APLPDEAKIC
    110 120 130 140 150
    TDKWLLKQIE LIAPQIIVPL GAVAAEFFLG EKVSITKVRG KWYEWHGIKV
    160 170 180 190 200
    FPMFHPAYLL RNPSRAPGSP KHLTWLDIQE VKRALDALPP KERRPVKAVS

    QEPLF
    Length:205
    Mass (Da):22,966
    Last modified:December 21, 2004 - 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:i74720211D889806F
    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
    AB109239 Genomic DNA Translation: BAC79245.1
    AP008226 Genomic DNA Translation: BAD70541.1

    NCBI Reference Sequences

    More...
    RefSeqi
    WP_011228142.1, NC_006461.1
    YP_143984.1, NC_006461.1

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    BAD70541; BAD70541; BAD70541

    Database of genes from NCBI RefSeq genomes

    More...
    GeneIDi
    3169183

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    ttj:TTHA0718

    Pathosystems Resource Integration Center (PATRIC)

    More...
    PATRICi
    fig|300852.9.peg.711

    <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
    AB109239 Genomic DNA Translation: BAC79245.1
    AP008226 Genomic DNA Translation: BAD70541.1
    RefSeqiWP_011228142.1, NC_006461.1
    YP_143984.1, NC_006461.1

    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
    1UI0X-ray1.50A1-205[»]
    1UI1X-ray2.80A1-205[»]
    ProteinModelPortaliQ5SKC5
    SMRiQ5SKC5
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi300852.TTHA0718

    Chemistry databases

    DrugBankiDB03419 Uracil

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiBAD70541; BAD70541; BAD70541
    GeneIDi3169183
    KEGGittj:TTHA0718
    PATRICifig|300852.9.peg.711

    Phylogenomic databases

    eggNOGiENOG4108UN4 Bacteria
    COG1573 LUCA
    HOGENOMiHOG000196501
    KOiK21929
    OMAiWLMWQDI
    PhylomeDBiQ5SKC5

    Enzyme and pathway databases

    BioCyciTTHE300852:G1GKC-735-MONOMER
    BRENDAi3.2.2.27 2305

    Family and domain databases

    CDDicd10030 UDG_F4_TTUDGA_like, 1 hit
    Gene3Di3.40.470.10, 1 hit
    InterProiView protein in InterPro
    IPR005273 Ura-DNA_glyco_family4
    IPR005122 Uracil-DNA_glycosylase-like
    IPR036895 Uracil-DNA_glycosylase-like_sf
    PfamiView protein in Pfam
    PF03167 UDG, 1 hit
    SMARTiView protein in SMART
    SM00986 UDG, 1 hit
    SUPFAMiSSF52141 SSF52141, 1 hit
    TIGRFAMsiTIGR00758 UDG_fam4, 1 hit

    ProtoNet; Automatic hierarchical classification of proteins

    More...
    ProtoNeti
    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 nameiUDGA_THET8
    <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: Q5SKC5
    Secondary accession number(s): Q7WYV4
    <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: March 15, 2017
    Last sequence update: December 21, 2004
    Last modified: December 5, 2018
    This is version 68 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, 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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