DNLI_PYRFU
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 03-AUG-2022, entry version 137.
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;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00407,
CC 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 EnsemblBacteria; AAL81759; AAL81759; 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 OMA; WLFEESY; -.
DR OrthoDB; 52275at2157; -.
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 Gene3D; 1.10.3260.10; -; 1.
DR Gene3D; 2.40.50.140; -; 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 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; SSF117018; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR TIGRFAMs; TIGR00574; dnl1; 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
