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O87703

- DNLJ_GEOSE

UniProt

O87703 - DNLJ_GEOSE

Protein

DNA ligase

Gene

ligA

Organism
Geobacillus stearothermophilus (Bacillus stearothermophilus)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 91 (01 Oct 2014)
      Sequence version 1 (01 Nov 1998)
      Previous versions | rss
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    Functioni

    DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA.UniRule annotation

    Catalytic activityi

    NAD+ + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + beta-nicotinamide D-ribonucleotide + (deoxyribonucleotide)(n+m).UniRule annotation

    Cofactori

    Magnesium or manganese.UniRule annotation

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei112 – 1121NADUniRule annotation
    Active sitei114 – 1141N6-AMP-lysine intermediate
    Binding sitei135 – 1351NADUniRule annotation
    Binding sitei169 – 1691NADUniRule annotation
    Binding sitei285 – 2851NADUniRule annotation
    Binding sitei309 – 3091NADUniRule annotation
    Metal bindingi403 – 4031ZincUniRule annotation
    Metal bindingi406 – 4061ZincUniRule annotation
    Metal bindingi421 – 4211ZincUniRule annotation
    Metal bindingi426 – 4261ZincUniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi34 – 385NADUniRule annotation
    Nucleotide bindingi83 – 842NADUniRule annotation

    GO - Molecular functioni

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

    GO - Biological processi

    1. DNA repair Source: UniProtKB-KW
    2. DNA replication Source: UniProtKB-KW

    Keywords - Molecular functioni

    Ligase

    Keywords - Biological processi

    DNA damage, DNA repair, DNA replication

    Keywords - Ligandi

    Magnesium, Manganese, Metal-binding, NAD, Zinc

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA ligaseUniRule annotation (EC:6.5.1.2UniRule annotation)
    Alternative name(s):
    Polydeoxyribonucleotide synthase [NAD(+)]UniRule annotation
    Gene namesi
    Name:ligAUniRule annotation
    Synonyms:lig
    OrganismiGeobacillus stearothermophilus (Bacillus stearothermophilus)
    Taxonomic identifieri1422 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeGeobacillus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 670670DNA ligasePRO_0000161737Add
    BLAST

    Proteomic databases

    PRIDEiO87703.

    Structurei

    Secondary structure

    1
    670
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi3 – 2523
    Helixi35 – 5016
    Helixi52 – 543
    Helixi60 – 634
    Helixi92 – 10413
    Beta strandi109 – 12517
    Beta strandi128 – 1347
    Beta strandi141 – 1433
    Helixi145 – 1495
    Beta strandi164 – 1718
    Helixi174 – 18613
    Helixi195 – 20410
    Helixi208 – 2136
    Beta strandi217 – 2237
    Turni224 – 2307
    Helixi234 – 24310
    Beta strandi253 – 2575
    Helixi258 – 27114
    Beta strandi279 – 2868
    Helixi289 – 2957
    Beta strandi299 – 3013
    Beta strandi305 – 3095

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1B04X-ray2.80A/B1-318[»]
    ProteinModelPortaliO87703.
    SMRiO87703. Positions 1-313.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO87703.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini589 – 67082BRCTUniRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the NAD-dependent DNA ligase family. LigA subfamily.UniRule annotation
    Contains 1 BRCT domain.UniRule annotation

    Family and domain databases

    Gene3Di2.40.50.140. 1 hit.
    3.40.50.10190. 1 hit.
    HAMAPiMF_01588. DNA_ligase_A.
    InterProiIPR001357. BRCT_dom.
    IPR018239. DNA_ligase_AS.
    IPR001679. DNAligase.
    IPR013839. DNAligase_adenylation.
    IPR013840. DNAligase_N.
    IPR000445. HhH_motif.
    IPR003583. Hlx-hairpin-Hlx_DNA-bd_motif.
    IPR012340. NA-bd_OB-fold.
    IPR004150. NAD_DNA_ligase_OB.
    IPR010994. RuvA_2-like.
    IPR004149. Znf_DNAligase_C4.
    [Graphical view]
    PfamiPF00533. BRCT. 1 hit.
    PF01653. DNA_ligase_aden. 1 hit.
    PF03120. DNA_ligase_OB. 1 hit.
    PF03119. DNA_ligase_ZBD. 1 hit.
    PF00633. HHH. 1 hit.
    [Graphical view]
    PIRSFiPIRSF001604. LigA. 1 hit.
    SMARTiSM00292. BRCT. 1 hit.
    SM00278. HhH1. 3 hits.
    SM00532. LIGANc. 1 hit.
    [Graphical view]
    SUPFAMiSSF47781. SSF47781. 1 hit.
    SSF50249. SSF50249. 1 hit.
    SSF52113. SSF52113. 1 hit.
    TIGRFAMsiTIGR00575. dnlj. 1 hit.
    PROSITEiPS50172. BRCT. 1 hit.
    PS01055. DNA_LIGASE_N1. 1 hit.
    PS01056. DNA_LIGASE_N2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    O87703-1 [UniParc]FASTAAdd to Basket

    « Hide

    MDRQQAERRA AELRELLNRY GYEYYVLDRP SVPDAEYDRL MQELIAIEEQ    50
    YPELKTSDSP TQRIGGPPLE AFRKVAHRVP MMSLANAFGE GDLRDFDRRV 100
    RQEVGEAAYV CELKIDGLAV SVRYEDGYFV QGATRGDGTT GEDITENLKT 150
    IRSLPLRLKE PVSLEARGEA FMPKASFLRL NEERKARGEE LFANPRNAAA 200
    GSLRQLDPKV AASRQLDLFV YGLADAEALG IASHSEALDY LQALGFKVNP 250
    ERRRCANIDE VIAFVSEWHD KRPQLPYEID GIVIKVDSFA QQRALGATAK 300
    SPRWAIAYKF PAEEVVTTLI GIEVNVGRTG VVTPTAILEP VRVAGTTVQR 350
    ATLHNEDFIR EKDIRIGDAV IIKKAGDIIP EVVGVVVDRR DGDETPFAMP 400
    THCPECESEL VRLEGEVALR CLNPNCPAQL RERLIHFASR AAMNIEGLGE 450
    KVVTQLFNAG LVRDVADLYC LTKEQLVGLE RMGEKSAANL LAAIEASKQN 500
    SLERLLFGLG IRYVGAKAAQ LLAEHFETME RLERATKEEL MAVPEIGEKM 550
    ADAITAFFAQ PEATELLQEL RAYGVNMAYK GPKRSAEAPA DSAFAGKTVV 600
    LTGKLASMSR NEAKEQIERL GGRVTGSVSR STDLVIAGED AGSKLEKAQQ 650
    LGIEIWDESR FLQEINRGKR 670
    Length:670
    Mass (Da):74,231
    Last modified:November 1, 1998 - v1
    Checksum:iB52462314CF9ACF5
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ011676 Genomic DNA. Translation: CAA09732.1.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ011676 Genomic DNA. Translation: CAA09732.1 .

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1B04 X-ray 2.80 A/B 1-318 [» ]
    ProteinModelPortali O87703.
    SMRi O87703. Positions 1-313.
    ModBasei Search...
    MobiDBi Search...

    Proteomic databases

    PRIDEi O87703.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Miscellaneous databases

    EvolutionaryTracei O87703.

    Family and domain databases

    Gene3Di 2.40.50.140. 1 hit.
    3.40.50.10190. 1 hit.
    HAMAPi MF_01588. DNA_ligase_A.
    InterProi IPR001357. BRCT_dom.
    IPR018239. DNA_ligase_AS.
    IPR001679. DNAligase.
    IPR013839. DNAligase_adenylation.
    IPR013840. DNAligase_N.
    IPR000445. HhH_motif.
    IPR003583. Hlx-hairpin-Hlx_DNA-bd_motif.
    IPR012340. NA-bd_OB-fold.
    IPR004150. NAD_DNA_ligase_OB.
    IPR010994. RuvA_2-like.
    IPR004149. Znf_DNAligase_C4.
    [Graphical view ]
    Pfami PF00533. BRCT. 1 hit.
    PF01653. DNA_ligase_aden. 1 hit.
    PF03120. DNA_ligase_OB. 1 hit.
    PF03119. DNA_ligase_ZBD. 1 hit.
    PF00633. HHH. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF001604. LigA. 1 hit.
    SMARTi SM00292. BRCT. 1 hit.
    SM00278. HhH1. 3 hits.
    SM00532. LIGANc. 1 hit.
    [Graphical view ]
    SUPFAMi SSF47781. SSF47781. 1 hit.
    SSF50249. SSF50249. 1 hit.
    SSF52113. SSF52113. 1 hit.
    TIGRFAMsi TIGR00575. dnlj. 1 hit.
    PROSITEi PS50172. BRCT. 1 hit.
    PS01055. DNA_LIGASE_N1. 1 hit.
    PS01056. DNA_LIGASE_N2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Nucleotide sequence, heterologous expression and novel purification of DNA ligase from Bacillus stearothermophilus."
      Brannigan J.A., Ashford S.R., Doherty A.J., Timson D.J., Wigley D.B.
      Biochim. Biophys. Acta 1432:413-418(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 29609 / DSM 2027 / NCA 1503 / NCIMB 8924.
    2. "Structure of the adenylation domain of an NAD+-dependent DNA ligase."
      Singleton M.R., Hakansson K., Timson D.J., Wigley D.B.
      Structure 7:35-42(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 1-318.

    Entry informationi

    Entry nameiDNLJ_GEOSE
    AccessioniPrimary (citable) accession number: O87703
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 30, 2000
    Last sequence update: November 1, 1998
    Last modified: October 1, 2014
    This is version 91 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

    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