ID   DNLI_PYRFU              Reviewed;         561 AA.
AC   P56709;
DT   30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT   30-MAY-2000, sequence version 1.
DT   27-MAR-2024, entry version 143.
DE   RecName: Full=DNA ligase {ECO:0000255|HAMAP-Rule:MF_00407};
DE            EC=6.5.1.1 {ECO:0000255|HAMAP-Rule:MF_00407, ECO:0000269|PubMed:16820169};
DE   AltName: Full=Polydeoxyribonucleotide synthase [ATP] {ECO:0000255|HAMAP-Rule:MF_00407};
GN   Name=lig {ECO:0000255|HAMAP-Rule:MF_00407}; OrderedLocusNames=PF1635;
OS   Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1).
OC   Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC   Pyrococcus.
OX   NCBI_TaxID=186497;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF N-TERMINUS.
RC   STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RA   Mathur E.J., Marsh E.J., Schoettlin W.E.;
RT   "Purified thermostable Pyrococcus furiosus DNA ligase.";
RL   Patent number US5700672, 23-DEC-1997.
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX   PubMed=10430560; DOI=10.1093/genetics/152.4.1299;
RA   Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M.,
RA   DiRuggiero J., Robb F.T.;
RT   "Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P.
RT   horikoshii inferred from complete genomic sequences.";
RL   Genetics 152:1299-1305(1999).
RN   [3]
RP   X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF MUTANT ALA-534 IN COMPLEX WITH
RP   AMP, ACTIVE SITE, CATALYTIC ACTIVITY, COFACTOR, AND MUTAGENESIS OF LYS-249;
RP   ARG-531 AND LYS-534.
RX   PubMed=16820169; DOI=10.1016/j.jmb.2006.05.062;
RA   Nishida H., Kiyonari S., Ishino Y., Morikawa K.;
RT   "The closed structure of an archaeal DNA ligase from Pyrococcus furiosus.";
RL   J. Mol. Biol. 360:956-967(2006).
CC   -!- FUNCTION: DNA ligase that seals nicks in double-stranded DNA during DNA
CC       replication, DNA recombination and DNA repair. {ECO:0000255|HAMAP-
CC       Rule:MF_00407}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-
CC         (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP +
CC         diphosphate.; EC=6.5.1.1; Evidence={ECO:0000255|HAMAP-Rule:MF_00407,
CC         ECO:0000269|PubMed:16820169};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_00407, ECO:0000305|PubMed:16820169};
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Temperature dependence:
CC         Optimum temperature is about 70 degrees Celsius. Active from 4 to 100
CC         degrees Celsius. Thermostable.;
CC   -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:16820169}.
CC   -!- SIMILARITY: Belongs to the ATP-dependent DNA ligase family.
CC       {ECO:0000255|HAMAP-Rule:MF_00407}.
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DR   EMBL; AE009950; AAL81759.1; -; Genomic_DNA.
DR   RefSeq; WP_011012782.1; NZ_CP023154.1.
DR   PDB; 2CFM; X-ray; 1.80 A; A=1-561.
DR   PDBsum; 2CFM; -.
DR   AlphaFoldDB; P56709; -.
DR   SMR; P56709; -.
DR   DIP; DIP-48778N; -.
DR   IntAct; P56709; 1.
DR   STRING; 186497.PF1635; -.
DR   PaxDb; 186497-PF1635; -.
DR   GeneID; 41713460; -.
DR   KEGG; pfu:PF1635; -.
DR   PATRIC; fig|186497.12.peg.1701; -.
DR   eggNOG; arCOG01347; Archaea.
DR   HOGENOM; CLU_005138_6_0_2; -.
DR   OrthoDB; 31274at2157; -.
DR   PhylomeDB; P56709; -.
DR   BRENDA; 6.5.1.1; 5243.
DR   EvolutionaryTrace; P56709; -.
DR   Proteomes; UP000001013; 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; cd07972; OBF_DNA_ligase_Arch_LigB; 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:SF7; DNA LIGASE; 1.
DR   PANTHER; PTHR45674; DNA LIGASE 1/3 FAMILY MEMBER; 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   3D-structure; ATP-binding; Cell cycle; Cell division;
KW   Direct protein sequencing; DNA damage; DNA recombination; DNA repair;
KW   DNA replication; Ligase; Magnesium; Metal-binding; Nucleotide-binding;
KW   Reference proteome.
FT   CHAIN           1..561
FT                   /note="DNA ligase"
FT                   /id="PRO_0000059613"
FT   ACT_SITE        249
FT                   /note="N6-AMP-lysine intermediate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407,
FT                   ECO:0000269|PubMed:16820169"
FT   BINDING         247
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407,
FT                   ECO:0000269|PubMed:16820169, ECO:0007744|PDB:2CFM"
FT   BINDING         254
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407,
FT                   ECO:0000269|PubMed:16820169, ECO:0007744|PDB:2CFM"
FT   BINDING         269
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407,
FT                   ECO:0000269|PubMed:16820169, ECO:0007744|PDB:2CFM"
FT   BINDING         299
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407,
FT                   ECO:0000269|PubMed:16820169, ECO:0007744|PDB:2CFM"
FT   BINDING         339
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407,
FT                   ECO:0000269|PubMed:16820169, ECO:0007744|PDB:2CFM"
FT   BINDING         414
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT   BINDING         420
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407,
FT                   ECO:0000269|PubMed:16820169, ECO:0007744|PDB:2CFM"
FT   MUTAGEN         249
FT                   /note="K->A: Loss of N6-AMP-lysine intermediate."
FT                   /evidence="ECO:0000269|PubMed:16820169"
FT   MUTAGEN         531
FT                   /note="R->A: Reduced ATP binding and enzyme activity; when
FT                   associated with A-534."
FT                   /evidence="ECO:0000269|PubMed:16820169"
FT   MUTAGEN         534
FT                   /note="K->A: Reduced ATP binding and enzyme activity; when
FT                   associated with A-531."
FT                   /evidence="ECO:0000269|PubMed:16820169"
FT   HELIX           3..14
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   HELIX           19..32
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   HELIX           35..37
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   TURN            38..40
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   HELIX           41..45
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   HELIX           62..73
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   HELIX           77..87
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   HELIX           90..101
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   TURN            102..104
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   HELIX           113..125
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   STRAND          128..130
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   HELIX           131..143
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   HELIX           148..159
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   HELIX           168..178
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   HELIX           183..193
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   HELIX           196..213
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   STRAND          226..231
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   HELIX           233..239
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   STRAND          244..249
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   STRAND          252..260
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   STRAND          263..267
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   HELIX           275..277
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   HELIX           279..288
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   STRAND          291..303
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   STRAND          307..309
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   HELIX           313..320
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   HELIX           325..331
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   STRAND          334..344
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   HELIX           354..364
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   STRAND          369..373
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   STRAND          376..380
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   HELIX           382..394
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   STRAND          399..403
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   STRAND          414..421
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   STRAND          428..437
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   HELIX           440..442
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   STRAND          445..454
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   TURN            456..458
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   STRAND          461..467
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   HELIX           473..483
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   HELIX           484..486
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   STRAND          487..491
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   STRAND          494..497
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   STRAND          502..506
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   STRAND          508..511
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   STRAND          514..516
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   STRAND          521..524
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   STRAND          526..530
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   HELIX           536..538
FT                   /evidence="ECO:0007829|PDB:2CFM"
FT   HELIX           542..557
FT                   /evidence="ECO:0007829|PDB:2CFM"
SQ   SEQUENCE   561 AA;  63773 MW;  534158525B9D24B2 CRC64;
     MRYLELAQLY QKLEKTTMKL IKTRLVADFL KKVPDDHLEF IPYLILGEVF PEWDERELGV
     GEKLLIKAVA MATGIDAKEI EESVKDTGDL GESIALAVKK KKQKSFFSQP LTIKRVYQTL
     VKVAETTGEG SQDKKVKYLA DLFMDAEPLE AKYLARTILG TMRTGVAEGL LRDAIAMAFH
     VKVELVERAY MLTSDFGYVA KIAKLEGNEG LAKVQVQLGK PIKPMLAQQA ASIRDALLEM
     GGEAEFEIKY DGARVQVHKD GSKIIVYSRR LENVTRAIPE IVEALKEAII PEKAIVEGEL
     VAIGENGRPL PFQYVLRRFR RKHNIEEMME KIPLELNLFD VLYVDGQSLI DTKFIDRRRT
     LEEIIKQNEK IKVAENLITK KVEEAEAFYK RALEMGHEGL MAKRLDAVYE PGNRGKKWLK
     IKPTMENLDL VIIGAEWGEG RRAHLFGSFI LGAYDPETGE FLEVGKVGSG FTDDDLVEFT
     KMLKPLIIKE EGKRVWLQPK VVIEVTYQEI QKSPKYRSGF ALRFPRFVAL RDDKGPEDAD
     TIERIAQLYE LQEKMKGKVE S
//