ID   DNLI_AERPE              Reviewed;         602 AA.
AC   Q9YD18;
DT   20-JUN-2001, integrated into UniProtKB/Swiss-Prot.
DT   20-JUN-2001, sequence version 2.
DT   27-MAR-2024, entry version 131.
DE   RecName: Full=DNA ligase {ECO:0000255|HAMAP-Rule:MF_00407, ECO:0000303|PubMed:12935888};
DE            EC=6.5.1.7 {ECO:0000305|PubMed:12935888};
DE   AltName: Full=Polydeoxyribonucleotide synthase [ATP/ADP] {ECO:0000305};
GN   Name=lig {ECO:0000255|HAMAP-Rule:MF_00407};
GN   OrderedLocusNames=APE_1094.1;
OS   Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 /
OS   K1).
OC   Archaea; Thermoproteota; Thermoprotei; Desulfurococcales;
OC   Desulfurococcaceae; Aeropyrum.
OX   NCBI_TaxID=272557;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1;
RX   PubMed=10382966; DOI=10.1093/dnares/6.2.83;
RA   Kawarabayasi Y., Hino Y., Horikawa H., Yamazaki S., Haikawa Y., Jin-no K.,
RA   Takahashi M., Sekine M., Baba S., Ankai A., Kosugi H., Hosoyama A.,
RA   Fukui S., Nagai Y., Nishijima K., Nakazawa H., Takamiya M., Masuda S.,
RA   Funahashi T., Tanaka T., Kudoh Y., Yamazaki J., Kushida N., Oguchi A.,
RA   Aoki K., Kubota K., Nakamura Y., Nomura N., Sako Y., Kikuchi H.;
RT   "Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon,
RT   Aeropyrum pernix K1.";
RL   DNA Res. 6:83-101(1999).
RN   [2]
RP   FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ACTIVITY REGULATION,
RP   BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RC   STRAIN=ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1;
RX   PubMed=12935888; DOI=10.1016/s0014-5793(03)00821-4;
RA   Jeon S.J., Ishikawa K.;
RT   "A novel ADP-dependent DNA ligase from Aeropyrum pernix K1.";
RL   FEBS Lett. 550:69-73(2003).
CC   -!- FUNCTION: DNA ligase that seals nicks in double-stranded DNA during DNA
CC       replication, DNA recombination and DNA repair. Can also use ADP, but
CC       not NAD(+). {ECO:0000269|PubMed:12935888}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-
CC         (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP +
CC         diphosphate.; EC=6.5.1.7; Evidence={ECO:0000255|HAMAP-Rule:MF_00407,
CC         ECO:0000269|PubMed:12935888};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=ADP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-
CC         (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + phosphate.;
CC         EC=6.5.1.7; Evidence={ECO:0000269|PubMed:12935888};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=GTP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-
CC         (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + GMP +
CC         diphosphate.; EC=6.5.1.7; Evidence={ECO:0000250|UniProtKB:A2BJX6};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000269|PubMed:12935888};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000269|PubMed:12935888};
CC       Note=Less active with Ca(2+) or Co(2+). Not active with Cu(2+), Zn(2+),
CC       Sr(2+) or Ni(2+). {ECO:0000269|PubMed:12935888};
CC   -!- ACTIVITY REGULATION: Inhibited in the presence of 100 mM KCl, NaCl or
CC       NH(4)Cl. {ECO:0000269|PubMed:12935888}.
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       pH dependence:
CC         Optimum pH is 7.5. {ECO:0000269|PubMed:12935888};
CC       Temperature dependence:
CC         Optimum temperature is 70 degrees Celsius.
CC         {ECO:0000269|PubMed:12935888};
CC   -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:12935888}.
CC   -!- SIMILARITY: Belongs to the ATP-dependent DNA ligase family.
CC       {ECO:0000255|HAMAP-Rule:MF_00407, ECO:0000305}.
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DR   EMBL; BA000002; BAA80079.2; -; Genomic_DNA.
DR   PIR; G72709; G72709.
DR   AlphaFoldDB; Q9YD18; -.
DR   SMR; Q9YD18; -.
DR   STRING; 272557.APE_1094.1; -.
DR   EnsemblBacteria; BAA80079; BAA80079; APE_1094.1.
DR   KEGG; ape:APE_1094.1; -.
DR   PATRIC; fig|272557.25.peg.768; -.
DR   eggNOG; arCOG01347; Archaea.
DR   BRENDA; 6.5.1.1; 171.
DR   Proteomes; UP000002518; Chromosome.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR   GO; GO:0003910; F:DNA ligase (ATP) activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0007049; P:cell cycle; IEA:UniProtKB-KW.
DR   GO; GO:0051301; P:cell division; IEA:UniProtKB-KW.
DR   GO; GO:0071897; P:DNA biosynthetic process; IEA:InterPro.
DR   GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-UniRule.
DR   GO; GO:0006281; P:DNA repair; IEA:UniProtKB-UniRule.
DR   GO; GO:0006260; P:DNA replication; IEA:UniProtKB-UniRule.
DR   CDD; cd07901; Adenylation_DNA_ligase_Arch_LigB; 1.
DR   CDD; cd07969; OBF_DNA_ligase_I; 1.
DR   Gene3D; 1.10.3260.10; DNA ligase, ATP-dependent, N-terminal domain; 1.
DR   Gene3D; 3.30.470.30; DNA ligase/mRNA capping enzyme; 1.
DR   Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 1.
DR   HAMAP; MF_00407; DNA_ligase; 1.
DR   InterPro; IPR022865; DNA_ligae_ATP-dep_bac/arc.
DR   InterPro; IPR000977; DNA_ligase_ATP-dep.
DR   InterPro; IPR012309; DNA_ligase_ATP-dep_C.
DR   InterPro; IPR012310; DNA_ligase_ATP-dep_cent.
DR   InterPro; IPR016059; DNA_ligase_ATP-dep_CS.
DR   InterPro; IPR012308; DNA_ligase_ATP-dep_N.
DR   InterPro; IPR036599; DNA_ligase_N_sf.
DR   InterPro; IPR012340; NA-bd_OB-fold.
DR   NCBIfam; TIGR00574; dnl1; 1.
DR   PANTHER; PTHR45674; DNA LIGASE 1/3 FAMILY MEMBER; 1.
DR   PANTHER; PTHR45674:SF9; DNA LIGASE 3; 1.
DR   Pfam; PF04679; DNA_ligase_A_C; 1.
DR   Pfam; PF01068; DNA_ligase_A_M; 1.
DR   Pfam; PF04675; DNA_ligase_A_N; 1.
DR   SUPFAM; SSF117018; ATP-dependent DNA ligase DNA-binding domain; 1.
DR   SUPFAM; SSF56091; DNA ligase/mRNA capping enzyme, catalytic domain; 1.
DR   SUPFAM; SSF50249; Nucleic acid-binding proteins; 1.
DR   PROSITE; PS00697; DNA_LIGASE_A1; 1.
DR   PROSITE; PS00333; DNA_LIGASE_A2; 1.
DR   PROSITE; PS50160; DNA_LIGASE_A3; 1.
PE   1: Evidence at protein level;
KW   ATP-binding; Cell cycle; Cell division; DNA damage; DNA recombination;
KW   DNA repair; DNA replication; Ligase; Magnesium; Manganese; Metal-binding;
KW   Nucleotide-binding; Reference proteome.
FT   CHAIN           1..602
FT                   /note="DNA ligase"
FT                   /id="PRO_0000059600"
FT   ACT_SITE        264
FT                   /note="N6-AMP-lysine intermediate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT   BINDING         262
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT   BINDING         269
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT   BINDING         284
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT   BINDING         314
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT   BINDING         354
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT   BINDING         431
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT   BINDING         437
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
SQ   SEQUENCE   602 AA;  67748 MW;  AD1DC7521FAFD814 CRC64;
     MPFKPVAEAF ASMERITSRT QLTLLLTRLF KSTPPGAIGI VVYLIQGKLG PDWKGLPELG
     VGEKLLVKAI ALAYKATEER VERLYKSVGD LGSVAERLSR EYRSRAARAV TLEAFMAGGG
     EALTVRRVYN TLYRIAMAQG EGSRDIKLRL LAGLLADAEP VEAKYIVRFV EGRLRVGVGD
     ATVLDALAMA FGGGAHARPV IERAYNLRAD LGYIAEVVAR EGVDALRGVK PQVGVPIRPM
     LAERGRDPAE ILRKVGGRAV VEYKYDGERA QIHKKDGEVY IYSRRLENIT RMFPDVVEMA
     RKGLKAGEAI VEGEIVAVDP DNYEIQPFQV LMQRKRKHDI HRVMREVPVA VFLFDALYVD
     GEDLTSKPLP ERRRRLKEIV VETPLWRLAE SIETSDPEEL WTFFLKAIEE GAEGVMVKAV
     HRDSVYTAGV RGWLWVKLKR DYKSEMMDTV DLVVVGAFYG RGKRGGKLSS LLMAAYDPDR
     DVFPTVCKVA TGFTDEELDR MNEMLKKHII PRKHPRVESR IEPDVWVEPA LVAEILGAEL
     TLSPMHTCCL NTVRPGVGIS IRFPRFIRWR DDKSPEDATT THELLEMYKR QLRRVEEPAE
     QV
//