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P56709

- DNLI_PYRFU

UniProt

P56709 - DNLI_PYRFU

Protein

DNA ligase

Gene

lig

Organism
Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 100 (01 Oct 2014)
      Sequence version 1 (30 May 2000)
      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).1 Publication

    Cofactori

    Magnesium.1 Publication

    Temperature dependencei

    Optimum temperature is about 70 degrees Celsius. Active from 4 to 100 degrees Celsius. Thermostable.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei247 – 2471ATP
    Active sitei249 – 2491N6-AMP-lysine intermediate1 Publication
    Binding sitei254 – 2541ATP
    Binding sitei269 – 2691ATP
    Binding sitei299 – 2991ATP
    Binding sitei339 – 3391ATP
    Binding sitei414 – 4141ATPBy similarity
    Binding sitei420 – 4201ATP

    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, Magnesium, Metal-binding, Nucleotide-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA ligase (EC:6.5.1.1)
    Alternative name(s):
    Pfu DNA ligase
    Polydeoxyribonucleotide synthase [ATP]
    Gene namesi
    Name:lig
    Ordered Locus Names:PF1635
    OrganismiPyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
    Taxonomic identifieri186497 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
    ProteomesiUP000001013: Chromosome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi249 – 2491K → A: Loss of N6-AMP-lysine intermediate. 1 Publication
    Mutagenesisi531 – 5311R → A: Reduced ATP binding and enzyme activity; when associated with A-534. 1 Publication
    Mutagenesisi534 – 5341K → A: Reduced ATP binding and enzyme activity; when associated with A-531. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 561561DNA ligasePRO_0000059613Add
    BLAST

    Proteomic databases

    PRIDEiP56709.

    Interactioni

    Subunit structurei

    Monomer.1 Publication

    Protein-protein interaction databases

    DIPiDIP-48778N.
    STRINGi186497.PF1635.

    Structurei

    Secondary structure

    1
    561
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi3 – 1412
    Helixi19 – 3214
    Helixi35 – 373
    Turni38 – 403
    Helixi41 – 455
    Helixi62 – 7312
    Helixi77 – 8711
    Helixi90 – 10112
    Turni102 – 1043
    Helixi113 – 12513
    Beta strandi128 – 1303
    Helixi131 – 14313
    Helixi148 – 15912
    Helixi168 – 17811
    Helixi183 – 19311
    Helixi196 – 21318
    Beta strandi226 – 2316
    Helixi233 – 2397
    Beta strandi244 – 2496
    Beta strandi252 – 2609
    Beta strandi263 – 2675
    Helixi275 – 2773
    Helixi279 – 28810
    Beta strandi291 – 30313
    Beta strandi307 – 3093
    Helixi313 – 3208
    Helixi325 – 3317
    Beta strandi334 – 34411
    Helixi354 – 36411
    Beta strandi369 – 3735
    Beta strandi376 – 3805
    Helixi382 – 39413
    Beta strandi399 – 4035
    Beta strandi414 – 4218
    Beta strandi428 – 43710
    Helixi440 – 4423
    Beta strandi445 – 45410
    Turni456 – 4583
    Beta strandi461 – 4677
    Helixi473 – 48311
    Helixi484 – 4863
    Beta strandi487 – 4915
    Beta strandi494 – 4974
    Beta strandi502 – 5065
    Beta strandi508 – 5114
    Beta strandi514 – 5163
    Beta strandi521 – 5244
    Beta strandi526 – 5305
    Helixi536 – 5383
    Helixi542 – 55716

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2CFMX-ray1.80A1-561[»]
    ProteinModelPortaliP56709.
    SMRiP56709. Positions 1-561.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP56709.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the ATP-dependent DNA ligase family.Curated

    Phylogenomic databases

    eggNOGiCOG1793.
    HOGENOMiHOG000036008.
    KOiK10747.
    OMAiARVQVHK.

    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.

    P56709-1 [UniParc]FASTAAdd to Basket

    « Hide

    MRYLELAQLY QKLEKTTMKL IKTRLVADFL KKVPDDHLEF IPYLILGEVF    50
    PEWDERELGV GEKLLIKAVA MATGIDAKEI EESVKDTGDL GESIALAVKK 100
    KKQKSFFSQP LTIKRVYQTL VKVAETTGEG SQDKKVKYLA DLFMDAEPLE 150
    AKYLARTILG TMRTGVAEGL LRDAIAMAFH VKVELVERAY MLTSDFGYVA 200
    KIAKLEGNEG LAKVQVQLGK PIKPMLAQQA ASIRDALLEM GGEAEFEIKY 250
    DGARVQVHKD GSKIIVYSRR LENVTRAIPE IVEALKEAII PEKAIVEGEL 300
    VAIGENGRPL PFQYVLRRFR RKHNIEEMME KIPLELNLFD VLYVDGQSLI 350
    DTKFIDRRRT LEEIIKQNEK IKVAENLITK KVEEAEAFYK RALEMGHEGL 400
    MAKRLDAVYE PGNRGKKWLK IKPTMENLDL VIIGAEWGEG RRAHLFGSFI 450
    LGAYDPETGE FLEVGKVGSG FTDDDLVEFT KMLKPLIIKE EGKRVWLQPK 500
    VVIEVTYQEI QKSPKYRSGF ALRFPRFVAL RDDKGPEDAD TIERIAQLYE 550
    LQEKMKGKVE S 561
    Length:561
    Mass (Da):63,773
    Last modified:May 30, 2000 - v1
    Checksum:i534158525B9D24B2
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE009950 Genomic DNA. Translation: AAL81759.1.
    RefSeqiNP_579364.1. NC_003413.1.
    WP_011012782.1. NC_003413.1.

    Genome annotation databases

    EnsemblBacteriaiAAL81759; AAL81759; PF1635.
    GeneIDi1469512.
    KEGGipfu:PF1635.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE009950 Genomic DNA. Translation: AAL81759.1 .
    RefSeqi NP_579364.1. NC_003413.1.
    WP_011012782.1. NC_003413.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2CFM X-ray 1.80 A 1-561 [» ]
    ProteinModelPortali P56709.
    SMRi P56709. Positions 1-561.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-48778N.
    STRINGi 186497.PF1635.

    Proteomic databases

    PRIDEi P56709.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAL81759 ; AAL81759 ; PF1635 .
    GeneIDi 1469512.
    KEGGi pfu:PF1635.

    Phylogenomic databases

    eggNOGi COG1793.
    HOGENOMi HOG000036008.
    KOi K10747.
    OMAi ARVQVHK.

    Miscellaneous databases

    EvolutionaryTracei P56709.

    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. "Purified thermostable Pyrococcus furiosus DNA ligase."
      Mathur E.J., Marsh E.J., Schoettlin W.E.
      Patent number US5700672, 23-DEC-1997
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF N-TERMINUS.
      Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
    2. "Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences."
      Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M., DiRuggiero J., Robb F.T.
      Genetics 152:1299-1305(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
    3. "The closed structure of an archaeal DNA ligase from Pyrococcus furiosus."
      Nishida H., Kiyonari S., Ishino Y., Morikawa K.
      J. Mol. Biol. 360:956-967(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF MUTANT ALA-534 IN COMPLEX WITH AMP, ACTIVE SITE, CATALYTIC ACTIVITY, COFACTOR, MUTAGENESIS OF LYS-249; ARG-531 AND LYS-534.

    Entry informationi

    Entry nameiDNLI_PYRFU
    AccessioniPrimary (citable) accession number: P56709
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 30, 2000
    Last sequence update: May 30, 2000
    Last modified: October 1, 2014
    This is version 100 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

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

    External Data

    Dasty 3