ID A0A941D3E0_9CAUL Unreviewed; 869 AA.
AC A0A941D3E0;
DT 22-FEB-2023, integrated into UniProtKB/TrEMBL.
DT 22-FEB-2023, sequence version 1.
DT 18-JUN-2025, entry version 11.
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:MBR7620171.1};
GN ORFNames=JKL49_12310 {ECO:0000313|EMBL:MBR7620171.1};
OS Phenylobacterium glaciei.
OC Bacteria; Pseudomonadati; Pseudomonadota; Alphaproteobacteria;
OC Caulobacterales; Caulobacteraceae; Phenylobacterium.
OX NCBI_TaxID=2803784 {ECO:0000313|EMBL:MBR7620171.1, ECO:0000313|Proteomes:UP000622580};
RN [1] {ECO:0000313|EMBL:MBR7620171.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=20VBR1 {ECO:0000313|EMBL:MBR7620171.1};
RA Thomas F.A., Krishnan K.P., Sinha R.K.;
RT "Draft genome assembly of strain Phenylobacterium sp. 20VBR1 using MiniION
RT and Illumina platforms.";
RL Submitted (APR-2021) 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 -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:MBR7620171.1}.
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DR EMBL; JAGSGD010000001; MBR7620171.1; -; Genomic_DNA.
DR RefSeq; WP_215340894.1; NZ_JAGSGD010000001.1.
DR Proteomes; UP000622580; 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:InterPro.
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 NCBIfam; NF004628; PRK05972.1; 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:MBR7620171.1};
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:UP000622580};
KW Transferase {ECO:0000256|ARBA:ARBA00022679}.
FT DOMAIN 337..469
FT /note="ATP-dependent DNA ligase family profile"
FT /evidence="ECO:0000259|PROSITE:PS50160"
FT REGION 541..570
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 869 AA; 94612 MW; 43003407A75E168B CRC64;
MATAKLDRYQ QMRDFQQTAE PSGRDAKVVT SERLRFVIQK HAATRLHFDL RLEHDGVFKS
WAVTRGPSLD PGDKRLAVQV EDHPLDYGDF EGTIPKGQYG GGTVQLWDRG YWAPEPGMED
IDKALKKGEL KFVMEGGRMH GSWVLVRLRD EGKRHNWLLI KHRDDAAVEG EGGALAAEDR
SIASERTMAQ IAAGEGRAAP PFMTASKTAA DAVWRTHQNA NSTAAASPRM GKAKDLKART
VATLPAFVEP QLCKSLEKPP QGPGWAHEIK FDGYRMQLRT VGGKATLKTR KGLDWSAKFQ
AIVQAGAGLA DSIIDGEVVA LDHTGAPDFA ALQAAISEGK TDDLIFFVFD LLFVDGEDLR
GLTLSARKDQ LKAMLAKAPA NVRYVDHFIT AGDAVLQSAC RMDLEGIISK RIDAPYRSGR
SDSWAKSKCR QGHEVVIGGW TTTGDAFRSL IAGVYRDGHL AHVGRIGTGF ARDKVDRLLP
KLKALETDKS PFGGKGAPKK ALGVHWVKPE LVAEIEYAGF TGDGSIRQAA FKGLRADKPA
QEVEAEVPAP AESADLATPT PRPAKTVTPK GSEVVMGVTI SSAAKALWPD AHDGSPVTKL
DLARYYEAVA EAILPHIKGR PCSIIRMPDG ITGGETFFQR HASRGSSSLF TEVEVSGDHK
PYLQIDRPQA LIAAAQIGAL ELHPWNCEPF KPEVPGRLVF DLDPAPDVDF DAVIEAAREV
RDRLEDLGLV SFCKTTGGKG LHVVTPLKAG KIDWPTAKAF ARDVCKAMAT DAPDRFLITM
AKKDRGGRIF LDYLRNDRMS TAVAPFSPRG RPGAPVSMPL TWSQVKKGLD PAKYTIRTVP
GLLNKLTAWE DYCDSERPLA VAIKRLGKV
//
