ID A0A0C5BVP5_9ARCH Unreviewed; 588 AA.
AC A0A0C5BVP5;
DT 29-APR-2015, integrated into UniProtKB/TrEMBL.
DT 29-APR-2015, sequence version 1.
DT 24-JAN-2024, entry version 33.
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 ECO:0000313|EMBL:AJM92331.1};
GN ORFNames=NPIRD3C_1119 {ECO:0000313|EMBL:AJM92331.1};
OS Nitrosopumilus piranensis.
OC Archaea; Nitrososphaerota; Nitrososphaeria; Nitrosopumilales;
OC Nitrosopumilaceae; Nitrosopumilus.
OX NCBI_TaxID=1582439 {ECO:0000313|EMBL:AJM92331.1, ECO:0000313|Proteomes:UP000032027};
RN [1] {ECO:0000313|Proteomes:UP000032027}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=D3C {ECO:0000313|Proteomes:UP000032027};
RA Bayer B., Vojvoda J., Offre P., Srivastava A., Elisabeth N., Garcia J.A.L.,
RA Schleper C., Herndl G.J.;
RT "Characterization of two novel Thaumarchaeota isolated from the Northern
RT Adriatic Sea.";
RL Submitted (FEB-2015) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:AJM92331.1, ECO:0000313|Proteomes:UP000032027}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=D3C {ECO:0000313|EMBL:AJM92331.1,
RC ECO:0000313|Proteomes:UP000032027};
RX PubMed=26528837; DOI=10.1038/ismej.2015.200;
RA Bayer B., Vojvoda J., Offre P., Alves R.J., Elisabeth N.H., Garcia J.A.,
RA Volland J.M., Srivastava A., Schleper C., Herndl G.J.;
RT "Physiological and genomic characterization of two novel marine
RT thaumarchaeal strains indicates niche differentiation.";
RL ISME J. 10:1051-1063(2016).
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|ARBA:ARBA00007572, ECO:0000256|HAMAP-Rule:MF_00407,
CC ECO:0000256|RuleBase:RU004196}.
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DR EMBL; CP010868; AJM92331.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A0C5BVP5; -.
DR STRING; 1582439.NPIRD3C_1119; -.
DR KEGG; nid:NPIRD3C_1119; -.
DR PATRIC; fig|1582439.9.peg.1154; -.
DR HOGENOM; CLU_005138_6_0_2; -.
DR OrthoDB; 31274at2157; -.
DR Proteomes; UP000032027; 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:SF4; DNA LIGASE 1; 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 330..463
FT /note="ATP-dependent DNA ligase family profile"
FT /evidence="ECO:0000259|PROSITE:PS50160"
FT ACT_SITE 252
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
FT BINDING 250
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
FT BINDING 257
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
FT BINDING 272
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
FT BINDING 302
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
FT BINDING 342
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
FT BINDING 417
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
FT BINDING 423
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
SQ SEQUENCE 588 AA; 66694 MW; 723DDE1EF366BDD1 CRC64;
MEFSVLADAF NKMESTRKRL ELTQYLVELF EKTPQEVISK IVYLLQGKLR PDFEGIELGV
AEKLAIRAIS KSSGIPIKKI EEEYRKGGDM GHAATIILEQ KTQTTFLVED ITVERVYETL
FKIAKLEGNR SQDMKMKYIS SLLNDASPLE ASFILKILLG TLRLGIAENT VMDALAIAFS
GNKENRKVLE HAYNVSSDLG KVAEILANDG LEGVEKFKII LFNPIRPMLA DRVKSEQEAI
EKMGEEFAAE YKLDGERVQL HIEGDKVVLF SRSLENISSY YPDIIEKIPK AIQAENIILE
AEAVAVNENT GEFLPFQELM HRRRKYKIEK AVTQYPITVN LFDILYCNGK SCLELDYKER
REKMEKVVKE DEFVKHIPMA IVKNENDIED FFENSINAGS EGLMLKMLDK PYQAGSRGSH
WLKLKREYQN ELGDSLDLVV IGGFFGKGRR TGSYGTLLLA TYEEDEDTFT SICKVGTGFS
DEDLDQLYQI LSPKVTIKKN PRIDSEMEAD VWFEPELVIE VVASEITLSP IHKAARDKVR
KGAGLALRFP KFTGKMRVEK MAEDASTNEE IITLYQGQKK VAHDKSLM
//