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Entry version 34 (18 Sep 2019)
Sequence version 1 (16 Apr 2014)
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Protein

DNA ligase B

Gene

ligB

Organism
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
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

DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair.UniRule annotation1 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 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

Mg2+UniRule annotation1 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=0.34 mM for ATP1 Publication

    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 sitei209ATPUniRule 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 sitei211N6-AMP-lysine intermediateUniRule annotation1
    Binding sitei216ATPUniRule annotation1
    Binding sitei231ATPUniRule annotation1
    Binding sitei260ATPUniRule annotation1
    Binding sitei300ATPUniRule annotation1
    Binding sitei372ATPUniRule annotation1
    Binding sitei378ATPUniRule 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

    <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 functionLigase
    Biological processCell cycle, Cell division, DNA damage, DNA recombination, DNA repair, DNA replication
    LigandATP-binding, Magnesium, Metal-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    MTBH37RV:G185E-7323-MONOMER

    SABIO-RK: Biochemical Reaction Kinetics Database

    More...
    SABIO-RKi
    P9WNV5

    <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:
    DNA ligase B (EC:6.5.1.1UniRule annotation1 Publication)
    Short name:
    LigB
    Alternative name(s):
    Polydeoxyribonucleotide synthase [ATP]UniRule 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:ligB
    Ordered Locus Names:Rv3062
    <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>OrganismiMycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
    <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 identifieri83332 [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 lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacteriumMycobacterium tuberculosis complex
    <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
    • UP000001584 <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

    Organism-specific databases

    Mycobacterium tuberculosis strain H37Rv genome database

    More...
    TubercuListi
    Rv3062

    <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

    Not essential for growth.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.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00003652311 – 507DNA ligase BAdd BLAST507

    Proteomic databases

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

    More...
    PaxDbi
    P9WNV5

    PRoteomics IDEntifications database

    More...
    PRIDEi
    P9WNV5

    <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
    83332.Rv3062

    <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
    P9WNV5

    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>Regioni1 – 172Not required for adenylyltransferase activity, required for nick joiningAdd BLAST172

    <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 ATP-dependent DNA ligase family.UniRule annotation

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...
    eggNOGi
    ENOG4107QIM Bacteria
    COG1793 LUCA

    KEGG Orthology (KO)

    More...
    KOi
    K10747

    Identification of Orthologs from Complete Genome Data

    More...
    OMAi
    WLFEESY

    Database for complete collections of gene phylogenies

    More...
    PhylomeDBi
    P9WNV5

    Family and domain databases

    Gene3D Structural and Functional Annotation of Protein Families

    More...
    Gene3Di
    1.10.3260.10, 1 hit

    HAMAP database of protein families

    More...
    HAMAPi
    MF_00407 DNA_ligase, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR022865 DNA_ligae_ATP-dep_bac/arc
    IPR000977 DNA_ligase_ATP-dep
    IPR012309 DNA_ligase_ATP-dep_C
    IPR012310 DNA_ligase_ATP-dep_cent
    IPR016059 DNA_ligase_ATP-dep_CS
    IPR012308 DNA_ligase_ATP-dep_N
    IPR036599 DNA_ligase_N_sf
    IPR012340 NA-bd_OB-fold

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF04679 DNA_ligase_A_C, 1 hit
    PF01068 DNA_ligase_A_M, 1 hit
    PF04675 DNA_ligase_A_N, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF117018 SSF117018, 1 hit
    SSF50249 SSF50249, 1 hit

    TIGRFAMs; a protein family database

    More...
    TIGRFAMsi
    TIGR00574 dnl1, 1 hit

    PROSITE; a protein domain and family database

    More...
    PROSITEi
    View protein in PROSITE
    PS00697 DNA_LIGASE_A1, 1 hit
    PS50160 DNA_LIGASE_A3, 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.

    P9WNV5-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MLLHDVAITS MDVAATSSRL TKVARIAALL HRAAPDTQLV TIIVSWLSGE
    60 70 80 90 100
    LPQRHIGVGW AALRSLPPPA PQPALTVTGV DATLSKIGTL PGKGSQAQRA
    110 120 130 140 150
    ALVAELFSAA TEAEQTFLLR LLGGELRQGA KGGIMADAVA QAAGLPAATV
    160 170 180 190 200
    QRAAMLGGDL AAAAAAGLSG AALDTFTLRV GRPIGPMLAQ TATSVHDALE
    210 220 230 240 250
    RHGGTTIFEA KLDGARVQIH RANDQVRIYT RSLDDVTARL PEVVEATLAL
    260 270 280 290 300
    PVRDLVADGE AIALCPDNRP QRFQVTASRF GRSVDVAAAR ATQPLSVFFF
    310 320 330 340 350
    DILHRDGTDL LEAPTTERLA ALDALVPARH RVDRLITSDP TDAANFLDAT
    360 370 380 390 400
    LAAGHEGVMA KAPAARYLAG RRGAGWLKVK PVHTLDLVVL AVEWGSGRRR
    410 420 430 440 450
    GKLSNIHLGA RDPATGGFVM VGKTFKGMTD AMLDWQTTRF HEIAVGPTDG
    460 470 480 490 500
    YVVQLRPEQV VEVALDGVQR SSRYPGGLAL RFARVVRYRA DKDPAEADTI

    DAVRALY
    Length:507
    Mass (Da):53,737
    Last modified:April 16, 2014 - 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:iA382F41A7B9E5741
    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
    AL123456 Genomic DNA Translation: CCP45871.1

    Protein sequence database of the Protein Information Resource

    More...
    PIRi
    G70649

    NCBI Reference Sequences

    More...
    RefSeqi
    NP_217578.1, NC_000962.3
    WP_003912069.1, NZ_NVQJ01000011.1

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    CCP45871; CCP45871; Rv3062

    Database of genes from NCBI RefSeq genomes

    More...
    GeneIDi
    887553

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    mtu:Rv3062
    mtv:RVBD_3062

    <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
    AL123456 Genomic DNA Translation: CCP45871.1
    PIRiG70649
    RefSeqiNP_217578.1, NC_000962.3
    WP_003912069.1, NZ_NVQJ01000011.1

    3D structure databases

    SMRiP9WNV5
    ModBaseiSearch...

    Protein-protein interaction databases

    STRINGi83332.Rv3062

    Proteomic databases

    PaxDbiP9WNV5
    PRIDEiP9WNV5

    Genome annotation databases

    EnsemblBacteriaiCCP45871; CCP45871; Rv3062
    GeneIDi887553
    KEGGimtu:Rv3062
    mtv:RVBD_3062

    Organism-specific databases

    TubercuListiRv3062

    Phylogenomic databases

    eggNOGiENOG4107QIM Bacteria
    COG1793 LUCA
    KOiK10747
    OMAiWLFEESY
    PhylomeDBiP9WNV5

    Enzyme and pathway databases

    BioCyciMTBH37RV:G185E-7323-MONOMER
    SABIO-RKiP9WNV5

    Family and domain databases

    Gene3Di1.10.3260.10, 1 hit
    HAMAPiMF_00407 DNA_ligase, 1 hit
    InterProiView protein in InterPro
    IPR022865 DNA_ligae_ATP-dep_bac/arc
    IPR000977 DNA_ligase_ATP-dep
    IPR012309 DNA_ligase_ATP-dep_C
    IPR012310 DNA_ligase_ATP-dep_cent
    IPR016059 DNA_ligase_ATP-dep_CS
    IPR012308 DNA_ligase_ATP-dep_N
    IPR036599 DNA_ligase_N_sf
    IPR012340 NA-bd_OB-fold
    PfamiView protein in Pfam
    PF04679 DNA_ligase_A_C, 1 hit
    PF01068 DNA_ligase_A_M, 1 hit
    PF04675 DNA_ligase_A_N, 1 hit
    SUPFAMiSSF117018 SSF117018, 1 hit
    SSF50249 SSF50249, 1 hit
    TIGRFAMsiTIGR00574 dnl1, 1 hit
    PROSITEiView protein in PROSITE
    PS00697 DNA_LIGASE_A1, 1 hit
    PS50160 DNA_LIGASE_A3, 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 nameiDNLI_MYCTU
    <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: P9WNV5
    Secondary accession number(s): L0TBG5, P95096, Q7D671
    <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: April 16, 2014
    Last sequence update: April 16, 2014
    Last modified: September 18, 2019
    This is version 34 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

    Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
    2. Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh
      Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh: entries and gene names
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