ID   Q1QR09_NITHX            Unreviewed;       866 AA.
AC   Q1QR09;
DT   16-MAY-2006, integrated into UniProtKB/TrEMBL.
DT   16-MAY-2006, sequence version 1.
DT   27-MAR-2024, entry version 98.
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=Nham_0448 {ECO:0000313|EMBL:ABE61338.1};
OS   Nitrobacter hamburgensis (strain DSM 10229 / NCIMB 13809 / X14).
OC   Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales;
OC   Nitrobacteraceae; Nitrobacter.
OX   NCBI_TaxID=323097 {ECO:0000313|EMBL:ABE61338.1, ECO:0000313|Proteomes:UP000001953};
RN   [1] {ECO:0000313|EMBL:ABE61338.1, ECO:0000313|Proteomes:UP000001953}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 10229 / NCIMB 13809 / X14
RC   {ECO:0000313|Proteomes:UP000001953};
RG   US DOE Joint Genome Institute;
RA   Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA   Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S.,
RA   Chain P., Malfatti S., Shin M., Vergez L., Schmutz J., Larimer F., Land M.,
RA   Hauser L., Kyrpides N., Ivanova N., Ward B., Arp D., Klotz M., Stein L.,
RA   O'Mullan G., Starkenburg S., Sayavedra L., Poret-Peterson A.T.,
RA   Gentry M.E., Bruce D., Richardson P.;
RT   "Complete sequence of chromosome of Nitrobacter hamburgensis X14.";
RL   Submitted (MAR-2006) 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};
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DR   EMBL; CP000319; ABE61338.1; -; Genomic_DNA.
DR   AlphaFoldDB; Q1QR09; -.
DR   STRING; 323097.Nham_0448; -.
DR   KEGG; nha:Nham_0448; -.
DR   eggNOG; COG1793; Bacteria.
DR   eggNOG; COG3285; Bacteria.
DR   HOGENOM; CLU_008325_0_1_5; -.
DR   Proteomes; UP000001953; 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:ABE61338.1};
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:UP000001953};
KW   Transferase {ECO:0000256|ARBA:ARBA00022679}.
FT   DOMAIN          314..409
FT                   /note="ATP-dependent DNA ligase family profile"
FT                   /evidence="ECO:0000259|PROSITE:PS50160"
FT   REGION          182..210
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          549..570
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ   SEQUENCE   866 AA;  94829 MW;  991B700C2D5F4819 CRC64;
     MHDATRLHYD FRLEYDGVFK SWAVTRGPSL DPAEKRLAVE VEDHPLDYGD FEGTIPKGQY
     GGGTVEIWDR GYWYADDPAK GLAKGDLKFA LMGEKLKGEW VLVRMKHDRS GGKRTNWLLI
     KHRDDYAKPG TGEEVLKHDR SVASGRTLRQ IAEGKGKAPE PFMMTRRIAG SDAVWDSNKG
     VAAKARDRNS KHSAVKTSAK PASARKRLPT KAKANAIKSE MPDFAGLQLC KTSTRPPSAD
     GWVHEIKFDG YRIQMRIENG DVTLKTRKGL DWTDKFPAIA SAATKLPDAI IDGEIVALNQ
     HGDPDFSAMQ AALSEDKTDE LVFFAFDLLF AEGEDLRPLS LLARKERLRQ LLGRSAKSAR
     ASIRYVEHFD ADGAQVLDTA REAGLEGIIS KRADEPYRAG RGGSWLKSKS RAGHEVVIGG
     WKTTSGKFRS LMAGVYNGDY LVYTGIVGTG YGRDTVKRIM PALKAAAASK SPFSGNNAPP
     GGPEVHWLKP ELVAEIEFAG WTADGMVRQA AFKGLRADKP AREVKAEAPS HATVPRLNAT
     RLAASAAAAA RADTTTSRQP RAPAARDRST VMGVAISHPD KALWPDAGDK QPVTKRDLAA
     YMETAGDWII QHIRGRPCSI VRAPDGIGGE TFFQRHAMPG LSDLVTEVKV SGDRKPYLQI
     DRVEGLIAVA QIGGLELHPW NCAPDQYDVP GRLVFDLDPA PDVAFPDVIA AAKEMKQRLE
     TLGLETFCKT TGGKGLHVVT PLAITQKNRL NWKQAKMFAQ AVCEQMATDT PDKYLITMSK
     KQREGKIFLD YLRNDTKSTA VAPLSPRARP GATVSMPLNW SQVKAGLDPK RFTLRTAPDL
     LKKSKAWSGY DEAARPLAAA IGKLVR
//