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C1CKI0

- DNLJ_STRZP

UniProt

C1CKI0 - DNLJ_STRZP

Protein

DNA ligase

Gene

ligA

Organism
Streptococcus pneumoniae (strain P1031)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 42 (01 Oct 2014)
      Sequence version 1 (26 May 2009)
      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 sitei107 – 1071NADUniRule annotation
    Active sitei109 – 1091N6-AMP-lysine intermediateUniRule annotation
    Binding sitei130 – 1301NADUniRule annotation
    Binding sitei164 – 1641NADUniRule annotation
    Binding sitei278 – 2781NADUniRule annotation
    Binding sitei302 – 3021NADUniRule annotation
    Metal bindingi395 – 3951ZincUniRule annotation
    Metal bindingi398 – 3981ZincUniRule annotation
    Metal bindingi413 – 4131ZincUniRule annotation
    Metal bindingi418 – 4181ZincUniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi29 – 335NADUniRule annotation
    Nucleotide bindingi78 – 792NADUniRule 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

    Enzyme and pathway databases

    BioCyciSPNE488223:GHE7-1100-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:SPP_1122
    OrganismiStreptococcus pneumoniae (strain P1031)
    Taxonomic identifieri488223 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeStreptococcus
    ProteomesiUP000002202: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 652652DNA ligasePRO_0000380487Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi488223.SPP_1122.

    Structurei

    Secondary structure

    1
    652
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi3 – 64
    Helixi38 – 458
    Helixi47 – 493
    Helixi55 – 584
    Beta strandi68 – 714
    Helixi85 – 9511
    Turni96 – 983
    Beta strandi104 – 1107
    Beta strandi112 – 1209
    Beta strandi123 – 1297
    Beta strandi133 – 1386
    Helixi140 – 1434
    Beta strandi159 – 1668
    Helixi169 – 18113
    Helixi190 – 1989
    Beta strandi199 – 2024
    Helixi203 – 2086
    Beta strandi212 – 22110
    Beta strandi223 – 2264
    Helixi227 – 23711
    Beta strandi246 – 2505
    Helixi251 – 26414
    Helixi265 – 2673
    Beta strandi268 – 2703
    Beta strandi272 – 2798
    Helixi282 – 2887
    Beta strandi292 – 30211

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4GLWX-ray2.00A/B1-305[»]
    ProteinModelPortaliC1CKI0.
    SMRiC1CKI0. Positions 2-304.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini577 – 65276BRCTUniRule 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.
    HOGENOMiHOG000218458.
    KOiK01972.
    OMAiSCGAKLA.
    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. 2 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.

    C1CKI0-1 [UniParc]FASTAAdd to Basket

    « Hide

    MNKRMNELVA LLNRYATEYY TSDNPSVSDS EYDRLYRELV ELETAYPEQV    50
    LADSPTHRVG GKVLDGFEKY SHQYPLYSLQ DAFSREELDA FDARVRKEVA 100
    HPTYICELKI DGLSISLTYE KGILVAGVTR GDGSIGENIT ENLKRVKDIP 150
    LTLPEELDIT VRGECYMPRA SFDQVNQARQ ENGEPEFANP RNAAAGTLRQ 200
    LDTAVVAKRN LATFLYQEAS PSTRDSQEKG LKYLEQLGFV VNPKRILAEN 250
    IDEIWNFIQE VGQERENLPY DIDGVVIKVN DLASQEELGF TVKAPKWAVA 300
    YKFPAEEKEA QLLSVDWTVG RTGVVTPTAN LTPVQLAGTT VSRATLHNVD 350
    YIAEKDIRKD DTVIVYKAGD IIPAVLRVVE SKRVSEEKLD IPTNCPSCNS 400
    DLLHFEDEVA LRCINPRCPA QIMEGLIHFA SRDAMNITGL GPSIVEKLFA 450
    ANLVKDVADI YRLQEEDFLL LEGVKEKSAA KLYQAIQASK ENSAEKLLFG 500
    LGIRHVGSKA SQLLLQYFHS IENLYQADSE EVASIESLGG VIAKSLQTYF 550
    ATEGSEILLR ELKETGVNLD YKGQTVVADA ALSGLTVVLT GKLERLKRSE 600
    AKSKLESLGA KVTGSVSKKT DLVVVGADAG SKLQKAQELG IQVRDEAWLE 650
    SL 652
    Length:652
    Mass (Da):72,276
    Last modified:May 26, 2009 - v1
    Checksum:iC2220D1F3504D47B
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000920 Genomic DNA. Translation: ACO21382.1.
    RefSeqiYP_002738268.1. NC_012467.1.

    Genome annotation databases

    EnsemblBacteriaiACO21382; ACO21382; SPP_1122.
    GeneIDi7682167.
    KEGGispp:SPP_1122.
    PATRICi32459541. VBIStrPne91701_1167.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000920 Genomic DNA. Translation: ACO21382.1 .
    RefSeqi YP_002738268.1. NC_012467.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    4GLW X-ray 2.00 A/B 1-305 [» ]
    ProteinModelPortali C1CKI0.
    SMRi C1CKI0. Positions 2-304.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 488223.SPP_1122.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ACO21382 ; ACO21382 ; SPP_1122 .
    GeneIDi 7682167.
    KEGGi spp:SPP_1122.
    PATRICi 32459541. VBIStrPne91701_1167.

    Phylogenomic databases

    eggNOGi COG0272.
    HOGENOMi HOG000218458.
    KOi K01972.
    OMAi SCGAKLA.
    OrthoDBi EOG6TTVM9.

    Enzyme and pathway databases

    BioCyci SPNE488223:GHE7-1100-MONOMER.

    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. 2 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. "Complete genome sequence of Streptococcus pneumoniae strain P1031."
      Hotopp J.D., Censini S., Masignani V., Covacci A., Tettelin H.
      Submitted (DEC-2007) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: P1031.

    Entry informationi

    Entry nameiDNLJ_STRZP
    AccessioniPrimary (citable) accession number: C1CKI0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 28, 2009
    Last sequence update: May 26, 2009
    Last modified: October 1, 2014
    This is version 42 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

    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