ID A0A086Y086_9RHOB Unreviewed; 841 AA.
AC A0A086Y086;
DT 29-OCT-2014, integrated into UniProtKB/TrEMBL.
DT 29-OCT-2014, sequence version 1.
DT 27-MAR-2024, entry version 40.
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:QBJ23967.1};
GN ORFNames=CN97_00390 {ECO:0000313|EMBL:KFI27686.1}, HmaOT1_06685
GN {ECO:0000313|EMBL:QBJ23967.1};
OS Haematobacter massiliensis.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales;
OC Paracoccaceae; Haematobacter.
OX NCBI_TaxID=195105 {ECO:0000313|EMBL:KFI27686.1, ECO:0000313|Proteomes:UP000028826};
RN [1] {ECO:0000313|EMBL:KFI27686.1, ECO:0000313|Proteomes:UP000028826}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CCUG 47968 {ECO:0000313|EMBL:KFI27686.1,
RC ECO:0000313|Proteomes:UP000028826};
RA Wang D., Wang G.;
RT "Genome of Haematobacter massiliensis CCUG 47968.";
RL Submitted (MAR-2014) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:QBJ23967.1, ECO:0000313|Proteomes:UP000291082}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=OT1 {ECO:0000313|EMBL:QBJ23967.1,
RC ECO:0000313|Proteomes:UP000291082};
RA Lee K.;
RT "The first complete genome sequence of Haematobacter massiliensis OT1
RT isolated from human skin.";
RL Submitted (JAN-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};
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DR EMBL; JGYG01000010; KFI27686.1; -; Genomic_DNA.
DR EMBL; CP035510; QBJ23967.1; -; Genomic_DNA.
DR RefSeq; WP_035712826.1; NZ_NIPY01000051.1.
DR AlphaFoldDB; A0A086Y086; -.
DR STRING; 195105.CN97_00390; -.
DR KEGG; hml:HmaOT1_06685; -.
DR eggNOG; COG1793; Bacteria.
DR eggNOG; COG3285; Bacteria.
DR OrthoDB; 9802472at2; -.
DR Proteomes; UP000028826; Unassembled WGS sequence.
DR Proteomes; UP000291082; 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; IPR022272; Lipocalin_CS.
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; PS00213; LIPOCALIN; 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:KFI27686.1};
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:UP000028826};
KW Transferase {ECO:0000256|ARBA:ARBA00022679}.
FT DOMAIN 33..138
FT /note="DNA ligase D 3'-phosphoesterase"
FT /evidence="ECO:0000259|Pfam:PF13298"
FT DOMAIN 251..431
FT /note="ATP-dependent DNA ligase family profile"
FT /evidence="ECO:0000259|Pfam:PF01068"
FT DOMAIN 451..544
FT /note="DNA ligase ATP-dependent C-terminal"
FT /evidence="ECO:0000259|Pfam:PF04679"
FT DOMAIN 578..826
FT /note="DNA ligase D polymerase"
FT /evidence="ECO:0000259|Pfam:PF21686"
FT REGION 164..243
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 208..243
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 841 AA; 92763 MW; 06A44BADECAAF4F5 CRC64;
MALETYNAKR DFSRTAEPQG KALAGEGGLY VIQKHDARRL HYDLRLELDG VLKSWAVTRG
PSLDPAEKRL AVEVEDHPLD YATFEGTIPK GQYGGGSVIV WDKGHWRPDF DPHAGLKKGH
LEFELDGEKL RGRWHLIRMK PRRGEKRVNW LLIKAEDDEA REAGDILKEE PRSVASGRTV
EEVGKGARAP TKASQGGVAG KAKKTAAPRE AGATETRQDK SENTADRPIT RVRTTKAEQG
EREKLPDFIE PMLATLARHP PSSGDWLHEI KFDGYRLLAR LEKGNVRLLT RSGLDWTERF
AGPLTEALEG LDARAALIDG ELVVEKPSGA SDFGALQADL SAGRADRFVY YAFDLLHLDG
YGLRSLPLVD RKAALERLIP GQGAVRFSAH FDDAGADVLA HACGLSLEGI ISKRSASAYV
SGRGRDWLKA KCALRQEFVI GGFTQSTATP QAIGSLALGV QEAGTLRYVG RVGTGFTAEV
AHDLWSRLTD LETRDNPFST RLDSTARRGL QHVRPELVAE VEFRAWTSDG RLRHASFRGL
REDKPAGDIV REEEAVERPE NVELTHPDRI YWPAEGVTKA DLADYYTRVW PRIAPFVTGR
ALALLRCPEG IEGPSFFQKH AWRGIPEQVR QVKDPKAPED PFVAIDDLDG LIALVQSAVL
EIHPWGSTLQ SWEKPDMIVM DLDPGEGITW PDIVSAAGKV RERLEDAGLA AFVKTSGGKG
LHVVAPLTPK ATWPSVKSFT KSLAEAMAAD EPDHFVATIS KAKRKGRILV DYLRNQRGMT
AVAPYSTRAR PGAAVSMPVP WEVLPEIGPQ DFTVLNIAEH LSSDPWEAFR DSAKPLPSRR
R
//
