ID D3SYT3_NATMM Unreviewed; 610 AA. AC D3SYT3; DT 20-APR-2010, integrated into UniProtKB/TrEMBL. DT 20-APR-2010, sequence version 1. DT 27-MAR-2024, entry version 79. 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=ligB {ECO:0000313|EMBL:ADD04194.1}; GN Synonyms=lig {ECO:0000256|HAMAP-Rule:MF_00407}; GN OrderedLocusNames=Nmag_0608 {ECO:0000313|EMBL:ADD04194.1}; GN ORFNames=C500_15590 {ECO:0000313|EMBL:ELY26599.1}; OS Natrialba magadii (strain ATCC 43099 / DSM 3394 / CCM 3739 / CIP 104546 / OS IAM 13178 / JCM 8861 / NBRC 102185 / NCIMB 2190 / MS3) (Natronobacterium OS magadii). OC Archaea; Euryarchaeota; Stenosarchaea group; Halobacteria; Natrialbales; OC Natrialbaceae; Natrialba. OX NCBI_TaxID=547559 {ECO:0000313|EMBL:ADD04194.1, ECO:0000313|Proteomes:UP000001879}; RN [1] {ECO:0000313|Proteomes:UP000001879} RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC 43099 / DSM 3394 / CCM 3739 / CIP 104546 / IAM 13178 / JCM RC 8861 / NBRC 102185 / NCIMB 2190 / MS3 RC {ECO:0000313|Proteomes:UP000001879}; RG US DOE Joint Genome Institute; RA Lucas S., Copeland A., Lapidus A., Cheng J.-F., Bruce D., Goodwin L., RA Pitluck S., Davenport K., Saunders E., Detter J.C., Han C., Tapia R., RA Land M., Hauser L., Kyrpides N., Mikhailova N., De Castro R.E., RA Maupin-Furlow J.A., Woyke T.; RT "Complete sequence of chromosome of Natrialba magadii ATCC 43099."; RL Submitted (FEB-2010) to the EMBL/GenBank/DDBJ databases. RN [2] {ECO:0000313|EMBL:ADD04194.1, ECO:0000313|Proteomes:UP000001879} RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC 43099 {ECO:0000313|EMBL:ADD04194.1}, and ATCC 43099 / DSM RC 3394 / CCM 3739 / CIP 104546 / IAM 13178 / JCM 8861 / NBRC 102185 / RC NCIMB 2190 / MS3 {ECO:0000313|Proteomes:UP000001879}; RX PubMed=22559199; DOI=10.1186/1471-2164-13-165; RA Siddaramappa S., Challacombe J.F., Decastro R.E., Pfeiffer F., Sastre D.E., RA Gimenez M.I., Paggi R.A., Detter J.C., Davenport K.W., Goodwin L.A., RA Kyrpides N., Tapia R., Pitluck S., Lucas S., Woyke T., Maupin-Furlow J.A.; RT "A comparative genomics perspective on the genetic content of the RT alkaliphilic haloarchaeon Natrialba magadii ATCC 43099T."; RL BMC Genomics 13:165-165(2012). RN [3] {ECO:0000313|EMBL:ELY26599.1, ECO:0000313|Proteomes:UP000011543} RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC 43099 / DSM 3394 / CCM 3739 / CIP 104546 / IAM 13178 / JCM RC 8861 / NBRC 102185 / NCIMB 2190 / MS3 RC {ECO:0000313|Proteomes:UP000011543}, and MS-3 RC {ECO:0000313|EMBL:ELY26599.1}; RX PubMed=25393412; DOI=10.1371/journal.pgen.1004784; RA Becker E.A., Seitzer P.M., Tritt A., Larsen D., Krusor M., Yao A.I., Wu D., RA Madern D., Eisen J.A., Darling A.E., Facciotti M.T.; RT "Phylogenetically driven sequencing of extremely halophilic archaea reveals RT strategies for static and dynamic osmo-response."; RL PLoS Genet. 10:E1004784-E1004784(2014). RN [4] {ECO:0000313|EMBL:ADD04194.1} RP NUCLEOTIDE SEQUENCE. RC STRAIN=ATCC 43099 {ECO:0000313|EMBL:ADD04194.1}; RA Pfeiffer F.; RL Submitted (SEP-2016) 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; Evidence={ECO:0000256|HAMAP- CC Rule:MF_00407}; CC -!- SIMILARITY: Belongs to the ATP-dependent DNA ligase family. CC {ECO:0000256|HAMAP-Rule:MF_00407, ECO:0000256|RuleBase:RU004196}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; CP001932; ADD04194.1; -; Genomic_DNA. DR EMBL; AOHS01000051; ELY26599.1; -; Genomic_DNA. DR RefSeq; WP_004216345.1; NZ_AOHS01000051.1. DR AlphaFoldDB; D3SYT3; -. DR STRING; 547559.Nmag_0608; -. DR PaxDb; 547559-Nmag_0608; -. DR GeneID; 8823435; -. DR KEGG; nmg:Nmag_0608; -. DR PATRIC; fig|547559.17.peg.3058; -. DR eggNOG; arCOG01347; Archaea. DR HOGENOM; CLU_005138_6_0_2; -. DR OrthoDB; 31274at2157; -. DR Proteomes; UP000001879; Chromosome. DR Proteomes; UP000011543; Unassembled WGS sequence. 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 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; 2. DR SUPFAM; SSF117018; ATP-dependent DNA ligase DNA-binding domain; 2. 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; 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}; Reference proteome {ECO:0000313|Proteomes:UP000001879}. FT DOMAIN 382..516 FT /note="ATP-dependent DNA ligase family profile" FT /evidence="ECO:0000259|PROSITE:PS50160" FT REGION 116..159 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 130..159 FT /note="Polar residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT ACT_SITE 294 FT /note="N6-AMP-lysine intermediate" FT /evidence="ECO:0000256|HAMAP-Rule:MF_00407" FT BINDING 292 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000256|HAMAP-Rule:MF_00407" FT BINDING 299 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000256|HAMAP-Rule:MF_00407" FT BINDING 325 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000256|HAMAP-Rule:MF_00407" FT BINDING 354 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000256|HAMAP-Rule:MF_00407" FT BINDING 394 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000256|HAMAP-Rule:MF_00407" FT BINDING 475 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000256|HAMAP-Rule:MF_00407" FT BINDING 481 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000256|HAMAP-Rule:MF_00407" SQ SEQUENCE 610 AA; 65823 MW; AAB053AF4CC701D6 CRC64; MEFATFADRA ATIEAESADL EIVAHVRDLL AEAGDDLPIV ARFVQGRVFP AWDSTTLDIG PNTCYEAIAR AAGTNVDADD VEERLADRGE IGAVAASYDF GGQQGLGAFM SGGGSGAGGA VDNNDDQDDR NNGGNGSNSG NDSNSSNDSN SSNGTGDLTV REINDTLTDL AAAEGSGSQD RKVDLLFGLF NRCSSDEARY LARLVLSEMR IGVGEGTVRD AIAEAFEVPQ EPVERALQVS NDYGQVAETA REDGVDGLDE IDLEIGRPVQ AMLAQAGTVT DALEEWDEAA VEWKYDGARI QLHYDPAGPG GPDGDSNGET HVFSRNMEAV TDALPEVVEF ADEHLDGPAI LDGEVVAIDD DGNPLPFQEV LKRFRRKHDV AKARENVSVR PVFFDCLHAD GDDLLEEPLV ERHNQLESVL AMGPQQEPEE IDGFSLLWVT DNPDEIEAVD ADALEAGHEG IMLKNPDSAY SPGRRGKNWQ KRKPDVETLD CVVTGAEWGE GRRATFLGTF ELSVRDGDDL ETVGKVATGI TDEKLEELTE LLEPHIVAED GTAVELEPAV VFEVGYEEIQ TSPTYSSGYA LRFPRFLGVR YDKDTAGAET LERLETLFES //