ID A0A1U7DKL4_9RHOB Unreviewed; 836 AA.
AC A0A1U7DKL4; A0A2M9DCE2;
DT 10-MAY-2017, integrated into UniProtKB/TrEMBL.
DT 10-MAY-2017, sequence version 1.
DT 27-MAR-2024, entry version 26.
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 ORFNames=BV394_12420 {ECO:0000313|EMBL:APX90433.1}, CLV77_2340
GN {ECO:0000313|EMBL:PJJ85470.1};
OS Brevirhabdus pacifica.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales;
OC Paracoccaceae; Brevirhabdus.
OX NCBI_TaxID=1267768 {ECO:0000313|EMBL:APX90433.1, ECO:0000313|Proteomes:UP000187266};
RN [1] {ECO:0000313|EMBL:APX90433.1, ECO:0000313|Proteomes:UP000187266}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DY6-4 {ECO:0000313|EMBL:APX90433.1,
RC ECO:0000313|Proteomes:UP000187266};
RA Wang X.;
RT "Genomic analysis of Xuhuaishuia manganoxidans DY6-4.";
RL Submitted (JAN-2017) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:PJJ85470.1, ECO:0000313|Proteomes:UP000229573}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 27767 {ECO:0000313|EMBL:PJJ85470.1,
RC ECO:0000313|Proteomes:UP000229573};
RA Goeker M.;
RT "Genomic Encyclopedia of Archaeal and Bacterial Type Strains, Phase II
RT (KMG-II): From Individual Species to Whole Genera.";
RL Submitted (NOV-2017) 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; CP019124; APX90433.1; -; Genomic_DNA.
DR EMBL; PGFI01000012; PJJ85470.1; -; Genomic_DNA.
DR RefSeq; WP_076980451.1; NZ_PGFI01000012.1.
DR AlphaFoldDB; A0A1U7DKL4; -.
DR STRING; 1267768.BV394_12420; -.
DR OrthoDB; 9802472at2; -.
DR Proteomes; UP000187266; Chromosome.
DR Proteomes; UP000229573; Unassembled WGS sequence.
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:APX90433.1};
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:UP000187266};
KW Transferase {ECO:0000256|ARBA:ARBA00022679}.
FT DOMAIN 307..420
FT /note="ATP-dependent DNA ligase family profile"
FT /evidence="ECO:0000259|PROSITE:PS50160"
FT REGION 505..544
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 505..537
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 836 AA; 92007 MW; 119544D241127E8E CRC64;
MTRLDRYLAK RDFAVTPEPD AQGTPSAMGL RFSMQKHAAT RLHFDLRLEW DGVLLSWAVT
KGPSLDPAEK RLAVRTEDHP LSYLQFEGTI PKDEYGGGTV MLWDLGWWQP LHDVDEGLKS
GKLHFNIHGQ RLTGGWALVR MRGRKASDKG RENWLMIKER DEAVVEGKAA EIGQAQSTGI
QSGRDFDAIA AGGKAAFPPR RTAARPKFRK PQLATLRDTV PEGDGWWHEL KLDGYRGQAA
IGKGGVRIWT RSGQDWTDRF AELVPWFERL DCASALIDGE IIAGAGHSGF GALQTALKHG
GPLAFQAFDL LELDGKTLTD LPLRDRREML DGLLSGLPAR AALASTTVIE GEGTAMLDAI
CQAGGEGLVA KRTDSPYRAG RSRSWIKVKC DKRAEFVIVG YQQSDKRGRP FSSLLLGTYE
RGKLHYRGKV GTGFSDEGMA ELAAAMAPLE VSKSALSDPD DAPARGVRWL RPELVAEVVY
GEITGDGRLR HSRYLGLRGD KPAKEVEMDE EVPARNRKGE KAASDAKTAK PEAKASRKAG
PKVAGVTISS PDRVVFEDTG TTKLELARYY AAVAPAMLDE TARRPLSLVR HPSGLSDPGF
FQKHVAPGFE DPIRKVAIDE ADGDDAEYMY VTSAGGLVTA VQMGTIEFHL WGAKVDRLDR
PDRMVLDLDP DEAVGFAELR AAAQDIREHL ADLGLECGLM LTGGKGVHIM VPLRRSNDWD
TVRGFARTFA TILAEREPQR FTATMSKARR KGRIFIDWLR NDRGNTAIAP YSVRARPGAP
VAMPIDWREL DHKRKLPRFD LSAAQDRAKN GPVAFPEPQS ITREVVDRLE VFASGE
//
