ID D5VSB3_METIM Unreviewed; 565 AA.
AC D5VSB3;
DT 13-JUL-2010, integrated into UniProtKB/TrEMBL.
DT 13-JUL-2010, sequence version 1.
DT 24-JAN-2024, entry version 66.
DE RecName: Full=DNA ligase {ECO:0000256|ARBA:ARBA00013308, ECO:0000256|HAMAP-Rule:MF_00407};
DE EC=6.5.1.1 {ECO:0000256|HAMAP-Rule:MF_00407};
DE AltName: Full=Polydeoxyribonucleotide synthase [ATP] {ECO:0000256|HAMAP-Rule:MF_00407};
GN Name=lig {ECO:0000256|HAMAP-Rule:MF_00407};
GN OrderedLocusNames=Metin_0801 {ECO:0000313|EMBL:ADG13466.1};
OS Methanocaldococcus infernus (strain DSM 11812 / JCM 15783 / ME).
OC Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC Methanocaldococcaceae; Methanocaldococcus.
OX NCBI_TaxID=573063 {ECO:0000313|EMBL:ADG13466.1, ECO:0000313|Proteomes:UP000002061};
RN [1] {ECO:0000313|EMBL:ADG13466.1, ECO:0000313|Proteomes:UP000002061}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 11812 / JCM 15783 / ME {ECO:0000313|Proteomes:UP000002061};
RG US DOE Joint Genome Institute;
RA Lucas S., Copeland A., Lapidus A., Cheng J.-F., Bruce D., Goodwin L.,
RA Pitluck S., Munk A.C., Detter J.C., Han C., Tapia R., Land M., Hauser L.,
RA Kyrpides N., Mikhailova N., Sieprawska-Lupa M., Whitman W.B., Woyke T.;
RT "Complete sequence of Methanocaldococcus infernus ME.";
RL Submitted (APR-2010) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: DNA ligase that seals nicks in double-stranded DNA during DNA
CC replication, DNA recombination and DNA repair. {ECO:0000256|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:0000256|HAMAP-Rule:MF_00407};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00407};
CC -!- SIMILARITY: Belongs to the ATP-dependent DNA ligase family.
CC {ECO:0000256|HAMAP-Rule:MF_00407, ECO:0000256|RuleBase:RU004196}.
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DR EMBL; CP002009; ADG13466.1; -; Genomic_DNA.
DR RefSeq; WP_013100212.1; NC_014122.1.
DR AlphaFoldDB; D5VSB3; -.
DR STRING; 573063.Metin_0801; -.
DR GeneID; 9131815; -.
DR KEGG; mif:Metin_0801; -.
DR eggNOG; arCOG01347; Archaea.
DR HOGENOM; CLU_005138_6_0_2; -.
DR OMA; WLFEESY; -.
DR OrthoDB; 31274at2157; -.
DR Proteomes; UP000002061; 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 3: Inferred from homology;
KW ATP-binding {ECO:0000256|ARBA:ARBA00022840, ECO:0000256|HAMAP-
KW Rule:MF_00407};
KW Cell cycle {ECO:0000256|ARBA:ARBA00023306, ECO:0000256|HAMAP-
KW Rule:MF_00407};
KW Cell division {ECO:0000256|ARBA:ARBA00022618, ECO:0000256|HAMAP-
KW Rule:MF_00407};
KW DNA damage {ECO:0000256|ARBA:ARBA00022763, ECO:0000256|HAMAP-
KW Rule:MF_00407};
KW DNA recombination {ECO:0000256|ARBA:ARBA00023172, ECO:0000256|HAMAP-
KW Rule:MF_00407};
KW DNA repair {ECO:0000256|ARBA:ARBA00023204, ECO:0000256|HAMAP-
KW Rule:MF_00407};
KW DNA replication {ECO:0000256|ARBA:ARBA00022705, ECO:0000256|HAMAP-
KW Rule:MF_00407};
KW Ligase {ECO:0000256|ARBA:ARBA00022598, ECO:0000256|HAMAP-Rule:MF_00407};
KW Magnesium {ECO:0000256|ARBA:ARBA00022842, ECO:0000256|HAMAP-Rule:MF_00407};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_00407};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|HAMAP-
KW Rule:MF_00407}.
FT DOMAIN 322..467
FT /note="ATP-dependent DNA ligase family profile"
FT /evidence="ECO:0000259|PROSITE:PS50160"
FT ACT_SITE 247
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
FT BINDING 245
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
FT BINDING 252
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
FT BINDING 267
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
FT BINDING 295
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
FT BINDING 334
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
FT BINDING 426
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
FT BINDING 432
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
SQ SEQUENCE 565 AA; 65984 MW; 8E31B1DA19ADCEB3 CRC64;
MLWKEVCEIF NKIENTTKRL DKRAYFIKLL EKVKDPEDLK RICYIAIGRV FPEYDERELG
VGEKLLINAI ISSGINKDKL YEKIKETGDI GLAAEKAKEE GKVKTLLFSP LTVKEVFETL
RKVAETEGEG SQKKKMRLIS SLFLRASPIE RRYLARLILG DMRIGMNIPT VLEALSIYFN
VPKEKLEKIY AVTNDIGLLA EKLMKNELDD KELNIKLFRP IKPMLAQLAP SIEEAIIEMG
HPQFETKYDG ARIQIHKKGD KVKIYSRKLE DVTHALPEIV NEIKKFKHDL IVEGECVAIE
EGRPRPFQDI LRRFRRKHDI GKAMKKINLR AYLFDLLYKD GESYIDKPFK ERRKALEELV
GYENDWRKER ERIERELKED KKIDISYKLV TNDPREAKEF YKWSLSIGHE GVMIKNLNAP
YTPGSRVRTM YKFKPTLENL DVVITKAKRG MGKRKDWYGS FEICVKDKDG NLQPIGYVGT
GLTEEDLQML KEMIDKIVVK DLGDEVIVKP EIVVEVAYEE IQKSDKYPCG YALRFPRIVR
FRFDKSIEDI NTLEDVERIY KLQRK
//