ID   D7A5M0_STAND            Unreviewed;       842 AA.
AC   D7A5M0;
DT   10-AUG-2010, integrated into UniProtKB/TrEMBL.
DT   10-AUG-2010, sequence version 1.
DT   27-MAR-2024, entry version 65.
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   OrderedLocusNames=Snov_0819 {ECO:0000313|EMBL:ADH88144.1};
OS   Starkeya novella (strain ATCC 8093 / DSM 506 / JCM 20403 / CCM 1077 / IAM
OS   12100 / NBRC 12443 / NCIMB 10456).
OC   Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales;
OC   Xanthobacteraceae; Ancylobacter.
OX   NCBI_TaxID=639283 {ECO:0000313|EMBL:ADH88144.1, ECO:0000313|Proteomes:UP000006633};
RN   [1] {ECO:0000313|EMBL:ADH88144.1, ECO:0000313|Proteomes:UP000006633}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 8093 / DSM 506 / JCM 20403 / CCM 1077 / IAM 12100 / NBRC
RC   12443 / NCIMB 10456 {ECO:0000313|Proteomes:UP000006633};
RX   PubMed=23450099; DOI=10.4056/sigs.3006378;
RA   Kappler U., Davenport K., Beatson S., Lucas S., Lapidus A., Copeland A.,
RA   Berry K.W., Glavina Del Rio T., Hammon N., Dalin E., Tice H., Pitluck S.,
RA   Richardson P., Bruce D., Goodwin L.A., Han C., Tapia R., Detter J.C.,
RA   Chang Y.J., Jeffries C.D., Land M., Hauser L., Kyrpides N.C., Goker M.,
RA   Ivanova N., Klenk H.P., Woyke T.;
RT   "Complete genome sequence of the facultatively chemolithoautotrophic and
RT   methylotrophic alpha Proteobacterium Starkeya novella type strain (ATCC
RT   8093(T)).";
RL   Stand. Genomic Sci. 7:44-58(2012).
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};
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DR   EMBL; CP002026; ADH88144.1; -; Genomic_DNA.
DR   RefSeq; WP_013165649.1; NC_014217.1.
DR   AlphaFoldDB; D7A5M0; -.
DR   STRING; 639283.Snov_0819; -.
DR   KEGG; sno:Snov_0819; -.
DR   eggNOG; COG1793; Bacteria.
DR   eggNOG; COG3285; Bacteria.
DR   HOGENOM; CLU_008325_0_1_5; -.
DR   OrthoDB; 9802472at2; -.
DR   Proteomes; UP000006633; 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; 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; MULTIFUNCTIONAL NON-HOMOLOGOUS END JOINING DNA REPAIR 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:ADH88144.1};
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   Transferase {ECO:0000256|ARBA:ARBA00022679}.
FT   DOMAIN          326..456
FT                   /note="ATP-dependent DNA ligase family profile"
FT                   /evidence="ECO:0000259|PROSITE:PS50160"
FT   REGION          1..25
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          190..222
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1..18
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ   SEQUENCE   842 AA;  92477 MW;  FBD74CBB0D841233 CRC64;
     MGLETYRRKR DFNTTSEPKG RTSRRAGNLY LIQKHDARRL HYDFRLEMDG VLKSWAVTRG
     PSLVPGEKRL AVHVEDHPLD YGSFEGTIPK GEYGGGTVML WDTGTWTPIG DAHVAYKKGH
     LEFELDGEKL HGRWHLVRMH PRPREKKENW LLIKGEDEFA RTEEQSDILE ELPDSVKTGR
     DLDAIAKDAP GWSSKTGRLR PAPKPKATPA KAKAASGGAA KRKTVAGAPL PDFIEPQLAT
     LVDKAPSGTR WVHEIKFDGY RLEVRIEDGE VRLLTRTGLD WTARFGSRLV EAFKALPLSN
     ALIDGELVVE GGNGASHFST LQADLSEERT DRFLFYAFDL LFLDGEDLRS KPLVERKAAL
     AKLLAGVPDP LRYSEHFDED GDVMLRHACR LSLEGLVSKL ADAPYRSGRS KDWRKSKCTE
     RQEFVIGGYV PSTVSNHAIG SLVLGVYEAG KLGGKLRHVG RVGTGYTARV AADLWKQLQP
     LARDKSPFAG KLAAEAARGV HFVEPTLVAE IEFRGWTGER NLRHASYRGL REDKPAAEVV
     QEGAPEMNAD RPPGSSVKLT HPDRIYWPED GVTKQGLVDY YTQVWPKIAP FIVARPLALL
     RCPDGIAEAC FFQKHAWRGI NKAVKLVPDP KDKGGEPLLT ISDFDGLIAL VQAGTLEIHP
     WGAPLAGLEK PDMLIFDLDP GPGVGWPEVI AAAKEVRARL EADEMAAFVK TSGGKGLHVV
     TPLSSKAGWA PAKEYAKAVA DAMAADDPDR FISVATKAKR GGRIFVDYLR NARGATAVAP
     YSSRARAGAA VSMPVTWAEL DQLASAAQYT VDNAPTRLAS LDADPWEDFR AAAKPLPAGK
     KR
//