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Q837V6

- DNLJ_ENTFA

UniProt

Q837V6 - DNLJ_ENTFA

Protein

DNA ligase

Gene

ligA

Organism
Enterococcus faecalis (strain ATCC 700802 / V583)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 89 (01 Oct 2014)
      Sequence version 1 (01 Jun 2003)
      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 sitei118 – 1181NAD
    Active sitei120 – 1201N6-AMP-lysine intermediate
    Binding sitei141 – 1411NAD
    Binding sitei175 – 1751NAD
    Binding sitei291 – 2911NAD
    Binding sitei315 – 3151NAD
    Metal bindingi409 – 4091ZincUniRule annotation
    Metal bindingi412 – 4121ZincUniRule annotation
    Metal bindingi427 – 4271ZincUniRule annotation
    Metal bindingi432 – 4321ZincUniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi39 – 435NAD
    Nucleotide bindingi88 – 914NAD

    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

    Enzyme and pathway databases

    BioCyciEFAE226185:GHI1-709-MONOMER.

    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
    Ordered Locus Names:EF_0722
    OrganismiEnterococcus faecalis (strain ATCC 700802 / V583)
    Taxonomic identifieri226185 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesEnterococcaceaeEnterococcus
    ProteomesiUP000001415: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 676676DNA ligasePRO_0000313228Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi226185.EF0722.

    Structurei

    Secondary structure

    1
    676
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi8 – 3023
    Beta strandi31 – 333
    Helixi39 – 5517
    Helixi57 – 593
    Helixi65 – 673
    Beta strandi79 – 813
    Helixi95 – 10915
    Beta strandi115 – 1217
    Beta strandi123 – 1319
    Beta strandi134 – 1407
    Beta strandi144 – 1496
    Helixi151 – 1555
    Beta strandi165 – 1673
    Beta strandi170 – 1778
    Helixi180 – 19213
    Helixi201 – 2099
    Helixi214 – 2196
    Beta strandi223 – 2308
    Helixi240 – 25011
    Beta strandi259 – 2635
    Helixi264 – 27714
    Helixi278 – 2803
    Beta strandi281 – 2833
    Beta strandi285 – 29410
    Helixi295 – 3017
    Beta strandi305 – 31511
    Helixi319 – 3213

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1TA8X-ray1.80A1-323[»]
    1TAEX-ray2.70A/B/C/D1-324[»]
    3BA8X-ray1.90A1-324[»]
    3BA9X-ray1.90A1-324[»]
    3BAAX-ray1.90A1-324[»]
    3BABX-ray2.50A1-324[»]
    4EEQX-ray2.10A1-323[»]
    4EFBX-ray2.20A1-323[»]
    4EFEX-ray2.00A1-323[»]
    4LH6X-ray1.65A1-323[»]
    4LH7X-ray1.90A1-323[»]
    DisProtiDP00326.
    ProteinModelPortaliQ837V6.
    SMRiQ837V6. Positions 4-324.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ837V6.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini595 – 67682BRCTUniRule annotationAdd
    BLAST

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiCOG0272.
    KOiK01972.
    OMAiPVEYLCE.
    OrthoDBiEOG6TTVM9.

    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.
    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.
    [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.

    Q837V6-1 [UniParc]FASTAAdd to Basket

    « Hide

    MEQQPLTLTA ATTRAQELRK QLNQYSHEYY VKDQPSVEDY VYDRLYKELV    50
    DIETEFPDLI TPDSPTQRVG GKVLSGFEKA PHDIPMYSLN DGFSKEDIFA 100
    FDERVRKAIG KPVAYCCELK IDGLAISLRY ENGVFVRGAT RGDGTVGENI 150
    TENLRTVRSV PMRLTEPISV EVRGECYMPK QSFVALNEER EENGQDIFAN 200
    PRNAAAGSLR QLDTKIVAKR NLNTFLYTVA DFGPMKAKTQ FEALEELSAI 250
    GFRTNPERQL CQSIDEVWAY IEEYHEKRST LPYEIDGIVI KVNEFALQDE 300
    LGFTVKAPRW AIAYKFPPEE AETVVEDIEW TIGRTGVVTP TAVMAPVRVA 350
    GTTVSRASLH NADFIQMKDI RLNDHVIIYK AGDIIPEVAQ VLVEKRAADS 400
    QPYEMPTHCP ICHSELVHLD EEVALRCINP KCPAQIKEGL NHFVSRNAMN 450
    IDGLGPRVLA QMYDKGLVKD VADLYFLTEE QLMTLDKIKE KSANNIYTAI 500
    QGSKENSVER LIFGLGIRHV GAKAAKILAE HFGDLPTLSR ATAEEIVALD 550
    SIGETIADSV VTYFENEEVH ELMAELEKAQ VNLTYKGLRT EQLAEVESPF 600
    KDKTVVLTGK LAQYTREEAK EKIENLGGKV TGSVSKKTDI VVAGEDAGSK 650
    LTKAESLGVT VWNEQEMVDA LDASHF 676
    Length:676
    Mass (Da):75,584
    Last modified:June 1, 2003 - v1
    Checksum:i9B6B93FD8DBB8E3B
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE016830 Genomic DNA. Translation: AAO80542.1.
    RefSeqiNP_814472.1. NC_004668.1.

    Genome annotation databases

    EnsemblBacteriaiAAO80542; AAO80542; EF_0722.
    GeneIDi1199621.
    KEGGiefa:EF0722.
    PATRICi21851834. VBIEntFae7065_0667.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE016830 Genomic DNA. Translation: AAO80542.1 .
    RefSeqi NP_814472.1. NC_004668.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1TA8 X-ray 1.80 A 1-323 [» ]
    1TAE X-ray 2.70 A/B/C/D 1-324 [» ]
    3BA8 X-ray 1.90 A 1-324 [» ]
    3BA9 X-ray 1.90 A 1-324 [» ]
    3BAA X-ray 1.90 A 1-324 [» ]
    3BAB X-ray 2.50 A 1-324 [» ]
    4EEQ X-ray 2.10 A 1-323 [» ]
    4EFB X-ray 2.20 A 1-323 [» ]
    4EFE X-ray 2.00 A 1-323 [» ]
    4LH6 X-ray 1.65 A 1-323 [» ]
    4LH7 X-ray 1.90 A 1-323 [» ]
    DisProti DP00326.
    ProteinModelPortali Q837V6.
    SMRi Q837V6. Positions 4-324.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 226185.EF0722.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAO80542 ; AAO80542 ; EF_0722 .
    GeneIDi 1199621.
    KEGGi efa:EF0722.
    PATRICi 21851834. VBIEntFae7065_0667.

    Phylogenomic databases

    eggNOGi COG0272.
    KOi K01972.
    OMAi PVEYLCE.
    OrthoDBi EOG6TTVM9.

    Enzyme and pathway databases

    BioCyci EFAE226185:GHI1-709-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei Q837V6.

    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.
    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.
    [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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 700802 / V583.
    2. "Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal."
      Gajiwala K.S., Pinko C.
      Structure 12:1449-1459(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 1-325 IN COMPLEXES WITH NAD AND NICOTINAMIDE NUCLEOTIDE.

    Entry informationi

    Entry nameiDNLJ_ENTFA
    AccessioniPrimary (citable) accession number: Q837V6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 15, 2008
    Last sequence update: June 1, 2003
    Last modified: October 1, 2014
    This is version 89 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, 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