ID A0A5B8L4X0_9HYPH Unreviewed; 817 AA.
AC A0A5B8L4X0;
DT 13-NOV-2019, integrated into UniProtKB/TrEMBL.
DT 13-NOV-2019, sequence version 1.
DT 02-APR-2025, entry version 24.
DE RecName: Full=DNA ligase (ATP) {ECO:0000256|ARBA:ARBA00012727};
DE EC=6.5.1.1 {ECO:0000256|ARBA:ARBA00012727};
DE AltName: Full=NHEJ DNA polymerase {ECO:0000256|ARBA:ARBA00029943};
GN Name=ligD {ECO:0000313|EMBL:QDZ03086.1};
GN ORFNames=FQ775_23470 {ECO:0000313|EMBL:QDZ03086.1};
OS Nitratireductor mangrovi.
OC Bacteria; Pseudomonadati; Pseudomonadota; Alphaproteobacteria;
OC Hyphomicrobiales; Phyllobacteriaceae; Nitratireductor.
OX NCBI_TaxID=2599600 {ECO:0000313|EMBL:QDZ03086.1, ECO:0000313|Proteomes:UP000321389};
RN [1] {ECO:0000313|Proteomes:UP000321389}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=SY7 {ECO:0000313|Proteomes:UP000321389};
RA Ye Y.;
RT "Nitratireductor sp. nov. isolated from mangrove soil.";
RL Submitted (JUL-2019) to the EMBL/GenBank/DDBJ databases.
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|ARBA:ARBA00034003};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000256|ARBA:ARBA00001936};
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; CP042301; QDZ03086.1; -; Genomic_DNA.
DR RefSeq; WP_146301719.1; NZ_CP042301.2.
DR AlphaFoldDB; A0A5B8L4X0; -.
DR KEGG; niy:FQ775_23470; -.
DR OrthoDB; 9802472at2; -.
DR Proteomes; UP000321389; Chromosome.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003910; F:DNA ligase (ATP) activity; IEA:UniProtKB-EC.
DR GO; GO:0003887; F:DNA-directed DNA polymerase activity; IEA:UniProtKB-KW.
DR GO; GO:0004527; F:exonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
DR GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
DR CDD; cd07906; Adenylation_DNA_ligase_LigD_LigC; 1.
DR CDD; cd07971; OBF_DNA_ligase_LigD; 1.
DR CDD; cd04862; PaeLigD_Pol_like; 1.
DR Gene3D; 3.30.1490.70; -; 1.
DR Gene3D; 3.30.470.30; DNA ligase/mRNA capping enzyme; 1.
DR Gene3D; 3.90.920.10; DNA primase, PRIM domain; 1.
DR Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 1.
DR InterPro; IPR012309; DNA_ligase_ATP-dep_C.
DR InterPro; IPR012310; DNA_ligase_ATP-dep_cent.
DR InterPro; IPR014146; LigD_ligase_dom.
DR InterPro; IPR014144; LigD_PE_domain.
DR InterPro; IPR014145; LigD_pol_dom.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR014143; NHEJ_ligase_prk.
DR InterPro; IPR052171; NHEJ_LigD.
DR InterPro; IPR033651; PaeLigD_Pol-like.
DR NCBIfam; TIGR02777; LigD_PE_dom; 1.
DR NCBIfam; TIGR02778; ligD_pol; 1.
DR NCBIfam; TIGR02779; NHEJ_ligase_lig; 1.
DR NCBIfam; TIGR02776; NHEJ_ligase_prk; 1.
DR PANTHER; PTHR42705; BIFUNCTIONAL NON-HOMOLOGOUS END JOINING PROTEIN LIGD; 1.
DR PANTHER; PTHR42705:SF2; BIFUNCTIONAL NON-HOMOLOGOUS END JOINING PROTEIN LIGD; 1.
DR Pfam; PF04679; DNA_ligase_A_C; 1.
DR Pfam; PF01068; DNA_ligase_A_M; 1.
DR Pfam; PF13298; LigD_N; 1.
DR Pfam; PF21686; LigD_Prim-Pol; 1.
DR SUPFAM; SSF56091; DNA ligase/mRNA capping enzyme, catalytic domain; 1.
DR SUPFAM; SSF50249; Nucleic acid-binding proteins; 1.
DR PROSITE; PS50160; DNA_LIGASE_A3; 1.
PE 4: Predicted;
KW ATP-binding {ECO:0000256|ARBA:ARBA00022840};
KW DNA damage {ECO:0000256|ARBA:ARBA00022763};
KW DNA recombination {ECO:0000256|ARBA:ARBA00023172};
KW DNA repair {ECO:0000256|ARBA:ARBA00023204};
KW DNA-binding {ECO:0000256|ARBA:ARBA00023125};
KW DNA-directed DNA polymerase {ECO:0000256|ARBA:ARBA00022932};
KW Exonuclease {ECO:0000256|ARBA:ARBA00022839};
KW Hydrolase {ECO:0000256|ARBA:ARBA00022801};
KW Ligase {ECO:0000256|ARBA:ARBA00022598, ECO:0000313|EMBL:QDZ03086.1};
KW Manganese {ECO:0000256|ARBA:ARBA00023211};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723};
KW Multifunctional enzyme {ECO:0000256|ARBA:ARBA00023268};
KW Nuclease {ECO:0000256|ARBA:ARBA00022722};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741};
KW Nucleotidyltransferase {ECO:0000256|ARBA:ARBA00022695};
KW Reference proteome {ECO:0000313|Proteomes:UP000321389};
KW Transferase {ECO:0000256|ARBA:ARBA00022679}.
FT DOMAIN 317..455
FT /note="ATP-dependent DNA ligase family profile"
FT /evidence="ECO:0000259|PROSITE:PS50160"
FT REGION 1..33
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 8..20
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 817 AA; 89291 MW; 71262231380FC450 CRC64;
MATQKLGDYQ RKRDFSRTGE PEGQETAASG NRFVMHKHSA SADHYDLRLE LDGVLKSWAV
PKGPSLNPDD KRLAVETEDH PLEYIDFEGV IPEGEYGGGP MIVWDTGVWA PMDDAEKSLA
AGAFKFRLAG AKLNGGWMLT RLKPKPGEGA KKNWLLFKER DRAADRELDI IEARPESVKS
GRRIEDLVAP ERLPAKPPKL VPGRLSGAVR SAMPERVSPQ LATPAERPPS DKDWLHEIKF
DGYRTIALVD EGKARLMTRK GLDWTKRYGD VGQAFAGLPC KEAVIDGEIV ALDDRGVSRF
SLLQQALSDG AGNRLVFYAF DLIHLDGWDL RKVSLVKRKD LLSRLLAGQV SARSPIQFSD
HVAGDGAALF DQASELGLEG IISKDARAPY REERTRSWLK VKALQSGDFV IAGYTVSEAA
EGLAALALGE WENGELQYRG KVGSGFDAAA LADLLNRLEP LSDGAANLDG APKDVIAVRP
VLTAHIHYAN RTADNMLRHA VYKGLREAEL SGTKAEPRER LITDADLASI WVTNPTRRLF
GKSGPTKLDI AVYYALVGDF MLPHILGRPV SLVRCPTGKP QDCFFQRHAF SGMPSSVATF
QSTNSDGETK SYLSVEGVKG YLALAQFGVV EFHIWGTTAK RLEKADRMVF DLDPGEGVEW
REMVEAAVHI KGELEAMGLA PFVKTSGGKG LHITVPVKAK LSWKQLHQRS GGIAAAIAAT
APDTFTTNMA KDKRRNRIFV DFHRNARGAT AVAPYSLRAR TNLPASTPLS WSDLESIDAP
EDLNYSSLPG LLTSSGDPWA DISDFAREMP PPSNAGA
//
