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Q9HHC4

- DNLI_THEKO

UniProt

Q9HHC4 - DNLI_THEKO

Protein

DNA ligase

Gene

lig

Organism
Thermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 97 (01 Oct 2014)
      Sequence version 2 (20 Jun 2001)
      Previous versions | rss
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    Functioni

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

    Catalytic activityi

    ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).

    Cofactori

    Magnesium.
    Binds 1 lipoyl cofactor covalently.By similarity

    pH dependencei

    Optimum pH is 8.0.

    Temperature dependencei

    Still active at 100 degrees Celsius. Thermostable.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei247 – 2471ATPBy similarity
    Active sitei249 – 2491N6-AMP-lysine intermediateBy similarity
    Binding sitei254 – 2541ATPBy similarity
    Binding sitei269 – 2691ATPBy similarity
    Binding sitei299 – 2991ATPBy similarity
    Binding sitei339 – 3391ATPBy similarity
    Binding sitei414 – 4141ATPBy similarity
    Binding sitei420 – 4201ATPBy similarity

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-HAMAP
    2. DNA binding Source: InterPro
    3. DNA ligase (ATP) activity Source: UniProtKB-HAMAP
    4. metal ion binding Source: UniProtKB-KW

    GO - Biological processi

    1. cell cycle Source: UniProtKB-KW
    2. cell division Source: UniProtKB-KW
    3. DNA ligation involved in DNA repair Source: InterPro
    4. DNA recombination Source: UniProtKB-HAMAP
    5. DNA replication Source: UniProtKB-HAMAP

    Keywords - Molecular functioni

    Ligase

    Keywords - Biological processi

    Cell cycle, Cell division, DNA damage, DNA recombination, DNA repair, DNA replication

    Keywords - Ligandi

    ATP-binding, Metal-binding, NAD, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciTKOD69014:GH72-2184-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA ligase (EC:6.5.1.1)
    Alternative name(s):
    Lig(Tk)
    Polydeoxyribonucleotide synthase [ATP]
    Gene namesi
    Name:lig
    Ordered Locus Names:TK2140
    OrganismiThermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
    Taxonomic identifieri69014 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaeThermococcus
    ProteomesiUP000000536: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 559559DNA ligasePRO_0000059615Add
    BLAST

    Interactioni

    Subunit structurei

    Monomer.

    Protein-protein interaction databases

    STRINGi69014.TK2140.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9HHC4.
    SMRiQ9HHC4. Positions 1-558.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the ATP-dependent DNA ligase family.Curated

    Phylogenomic databases

    eggNOGiCOG1793.
    HOGENOMiHOG000036008.
    KOiK10747.

    Family and domain databases

    Gene3Di1.10.3260.10. 1 hit.
    2.40.50.140. 1 hit.
    HAMAPiMF_00407. DNA_ligase.
    InterProiIPR022865. 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.
    IPR012340. NA-bd_OB-fold.
    [Graphical view]
    PfamiPF04679. DNA_ligase_A_C. 1 hit.
    PF01068. DNA_ligase_A_M. 1 hit.
    PF04675. DNA_ligase_A_N. 1 hit.
    [Graphical view]
    SUPFAMiSSF117018. SSF117018. 1 hit.
    SSF50249. SSF50249. 1 hit.
    TIGRFAMsiTIGR00574. dnl1. 1 hit.
    PROSITEiPS00697. DNA_LIGASE_A1. 1 hit.
    PS00333. DNA_LIGASE_A2. 1 hit.
    PS50160. DNA_LIGASE_A3. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q9HHC4-1 [UniParc]FASTAAdd to Basket

    « Hide

    MRYSELADLY RRLEKTTLKT LKTKFVADFL KKTPDELLEI VPYLILGKVF    50
    PDWDERELGV GEKLLIKAVS MATGVPEKEI EDSVRDTGDL GESVALAIKK 100
    KKQKSFFSQP LTIKRVYDTF VKIAEAQGEG SQDRKMKYLA NLFMDAEPEE 150
    GKYLARTVLG TMRTGVAEGI LRDAIAEAFR VKPELVERAY MLTSDFGYVA 200
    KIAKLEGNEG LSKVRIQIGK PIRPMLAQNA ASVKDALIEM GGEAAFEIKY 250
    DGARVQVHKD GDKVIVYSRR LENVTRSIPE VIEAIKAALK PEKAIVEGEL 300
    VAVGENGRPR PFQYVLRRFR RKYNIDEMIE KIPLELNLFD VMFVDGESLI 350
    ETKFIDRRNK LEEIVKESEK IKLAEQLITK KVEEAEAFYR RALELGHEGL 400
    MAKRLDSIYE PGNRGKKWLK IKPTMENLDL VIIGAEWGEG RRAHLLGSFL 450
    VAAYDPHSGE FLPVGKVGSG FTDEDLVEFT KMLKPYIVRQ EGKFVEIEPK 500
    FVIEVTYQEI QKSPKYKSGF ALRFPRYVAL REDKSPEEAD TIERVAELYE 550
    LQERFKAKK 559
    Length:559
    Mass (Da):63,749
    Last modified:June 20, 2001 - v2
    Checksum:i91AB32542E03D20D
    GO

    Sequence cautioni

    The sequence BAB15949.1 differs from that shown. Reason: Erroneous initiation.
    The sequence BAD86329.1 differs from that shown. Reason: Erroneous initiation.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB042527 Genomic DNA. Translation: BAB15949.1. Different initiation.
    AP006878 Genomic DNA. Translation: BAD86329.1. Different initiation.
    RefSeqiYP_184553.1. NC_006624.1.

    Genome annotation databases

    EnsemblBacteriaiBAD86329; BAD86329; TK2140.
    GeneIDi3235455.
    KEGGitko:TK2140.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB042527 Genomic DNA. Translation: BAB15949.1 . Different initiation.
    AP006878 Genomic DNA. Translation: BAD86329.1 . Different initiation.
    RefSeqi YP_184553.1. NC_006624.1.

    3D structure databases

    ProteinModelPortali Q9HHC4.
    SMRi Q9HHC4. Positions 1-558.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 69014.TK2140.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAD86329 ; BAD86329 ; TK2140 .
    GeneIDi 3235455.
    KEGGi tko:TK2140.

    Phylogenomic databases

    eggNOGi COG1793.
    HOGENOMi HOG000036008.
    KOi K10747.

    Enzyme and pathway databases

    BioCyci TKOD69014:GH72-2184-MONOMER.

    Family and domain databases

    Gene3Di 1.10.3260.10. 1 hit.
    2.40.50.140. 1 hit.
    HAMAPi MF_00407. DNA_ligase.
    InterProi 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.
    IPR012340. NA-bd_OB-fold.
    [Graphical view ]
    Pfami PF04679. DNA_ligase_A_C. 1 hit.
    PF01068. DNA_ligase_A_M. 1 hit.
    PF04675. DNA_ligase_A_N. 1 hit.
    [Graphical view ]
    SUPFAMi SSF117018. SSF117018. 1 hit.
    SSF50249. SSF50249. 1 hit.
    TIGRFAMsi TIGR00574. dnl1. 1 hit.
    PROSITEi PS00697. DNA_LIGASE_A1. 1 hit.
    PS00333. DNA_LIGASE_A2. 1 hit.
    PS50160. DNA_LIGASE_A3. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "A DNA ligase from a hyperthermophilic archaeon with unique cofactor specificity."
      Nakatani M., Ezaki S., Atomi H., Imanaka T.
      J. Bacteriol. 182:6424-6433(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
      Strain: ATCC BAA-918 / JCM 12380 / KOD1.
    2. "Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes."
      Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T.
      Genome Res. 15:352-363(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC BAA-918 / JCM 12380 / KOD1.

    Entry informationi

    Entry nameiDNLI_THEKO
    AccessioniPrimary (citable) accession number: Q9HHC4
    Secondary accession number(s): Q5JHF2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 20, 2001
    Last sequence update: June 20, 2001
    Last modified: October 1, 2014
    This is version 97 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Can also use NAD, but less efficiently than ATP.

    Keywords - Technical termi

    Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3