DNLJ_HAMD5
ID DNLJ_HAMD5 Reviewed; 702 AA.
AC C4K4K4;
DT 01-SEP-2009, integrated into UniProtKB/Swiss-Prot.
DT 07-JUL-2009, sequence version 1.
DT 03-AUG-2022, entry version 69.
DE RecName: Full=DNA ligase {ECO:0000255|HAMAP-Rule:MF_01588};
DE EC=6.5.1.2 {ECO:0000255|HAMAP-Rule:MF_01588};
DE AltName: Full=Polydeoxyribonucleotide synthase [NAD(+)] {ECO:0000255|HAMAP-Rule:MF_01588};
GN Name=ligA {ECO:0000255|HAMAP-Rule:MF_01588}; OrderedLocusNames=HDEF_0769;
OS Hamiltonella defensa subsp. Acyrthosiphon pisum (strain 5AT).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; aphid secondary symbionts; Candidatus Hamiltonella.
OX NCBI_TaxID=572265;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=5AT;
RX PubMed=19451630; DOI=10.1073/pnas.0900194106;
RA Degnan P.H., Yu Y., Sisneros N., Wing R.A., Moran N.A.;
RT "Hamiltonella defensa, genome evolution of protective bacterial
RT endosymbiont from pathogenic ancestors.";
RL Proc. Natl. Acad. Sci. U.S.A. 106:9063-9068(2009).
CC -!- FUNCTION: DNA ligase that catalyzes the formation of phosphodiester
CC linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-
CC stranded DNA using NAD as a coenzyme and as the energy source for the
CC reaction. It is essential for DNA replication and repair of damaged
CC DNA. {ECO:0000255|HAMAP-Rule:MF_01588}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=NAD(+) + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-
CC (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + beta-
CC nicotinamide D-nucleotide.; EC=6.5.1.2; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01588};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01588};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01588};
CC -!- SIMILARITY: Belongs to the NAD-dependent DNA ligase family. LigA
CC subfamily. {ECO:0000255|HAMAP-Rule:MF_01588}.
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DR EMBL; CP001277; ACQ67497.1; -; Genomic_DNA.
DR RefSeq; WP_015873317.1; NC_012751.1.
DR AlphaFoldDB; C4K4K4; -.
DR SMR; C4K4K4; -.
DR STRING; 572265.HDEF_0769; -.
DR PRIDE; C4K4K4; -.
DR EnsemblBacteria; ACQ67497; ACQ67497; HDEF_0769.
DR GeneID; 66260611; -.
DR KEGG; hde:HDEF_0769; -.
DR eggNOG; COG0272; Bacteria.
DR HOGENOM; CLU_007764_2_1_6; -.
DR OMA; HDVEHEI; -.
DR Proteomes; UP000002334; Chromosome.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0003911; F:DNA ligase (NAD+) activity; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
DR GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
DR CDD; cd00114; LIGANc; 1.
DR Gene3D; 2.40.50.140; -; 1.
DR Gene3D; 3.40.50.10190; -; 1.
DR HAMAP; MF_01588; DNA_ligase_A; 1.
DR InterPro; IPR001357; BRCT_dom.
DR InterPro; IPR036420; BRCT_dom_sf.
DR InterPro; IPR041663; DisA/LigA_HHH.
DR InterPro; IPR018239; DNA_ligase_AS.
DR InterPro; IPR033136; DNA_ligase_CS.
DR InterPro; IPR001679; DNAligase.
DR InterPro; IPR013839; DNAligase_adenylation.
DR InterPro; IPR013840; DNAligase_N.
DR InterPro; IPR003583; Hlx-hairpin-Hlx_DNA-bd_motif.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR004150; NAD_DNA_ligase_OB.
DR InterPro; IPR010994; RuvA_2-like.
DR InterPro; IPR004149; Znf_DNAligase_C4.
DR Pfam; PF00533; BRCT; 1.
DR Pfam; PF01653; DNA_ligase_aden; 2.
DR Pfam; PF03120; DNA_ligase_OB; 1.
DR Pfam; PF03119; DNA_ligase_ZBD; 1.
DR Pfam; PF12826; HHH_2; 1.
DR PIRSF; PIRSF001604; LigA; 1.
DR SMART; SM00292; BRCT; 1.
DR SMART; SM00278; HhH1; 4.
DR SMART; SM00532; LIGANc; 1.
DR SUPFAM; SSF47781; SSF47781; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR SUPFAM; SSF52113; SSF52113; 1.
DR TIGRFAMs; TIGR00575; dnlj; 1.
DR PROSITE; PS50172; BRCT; 1.
DR PROSITE; PS01055; DNA_LIGASE_N1; 1.
DR PROSITE; PS01056; DNA_LIGASE_N2; 1.
PE 3: Inferred from homology;
KW DNA damage; DNA repair; DNA replication; Ligase; Magnesium; Manganese;
KW Metal-binding; NAD; Reference proteome; Zinc.
FT CHAIN 1..702
FT /note="DNA ligase"
FT /id="PRO_0000381944"
FT DOMAIN 616..702
FT /note="BRCT"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT REGION 104..125
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 105..119
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 141
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 32..36
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 81..82
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 139
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 162
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 199
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 316
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 340
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 434
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 437
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 452
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 458
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
SQ SEQUENCE 702 AA; 78091 MW; 897ED08DE2760D1C CRC64;
MKSMLEKINQ LRDVLKHHEY LYHVNDAPEI TDAEYDALLE KLREWESQYP ELMNPDSPTQ
KVGASPSTAF KPVTHQVPML SLDNVFDEKG FLAFNKRVSE RLEAESSAQK ASLNPLVRDS
DQKNRSEKNV QEALTFCCEL KLDGLAVSLI YEKGELTQAA TRGNGFQGEN ITHNIRTIQS
IPLRLKGKAL PQRIEIRGEV YMPQAGFEKL NKQARANHEK IFSNPRNAAA GSLRQLDPHI
TAQRPLNFFC YGVGLLEGGV LPQSHIQRLM QLKAWGLPVH DRITLCTGAE QVMAFYQEIA
QARATLGFDI DGIVIKVDDV LLQEKLGFLA KAPRWATAFK FPAQEKTTQV LGVEFQVGRT
GALTPVARLE PVELGGALVS NANLHNADEI ARLGLRIGDT VVVRRAGDVI PQIVNVIIES
RPQNTVEIIF PHHCPICKSV AKRIEGEAVI RCTGGLFCPA QRKEALKHFV ARRALDIEGL
GDKIIHQLVD KKYVQNPADL FHLTSEKLLS LKRMREKSAQ NLLNSLKKSQ KTTFARFLYA
LGIREVGETT AANLALYFGQ LDLLRKADIE TLKKVPDVGE VVAKNLVDFF GNEHHQQVIS
ALESVLDWPD PEPIEKPNHP FRDKTVVLTG SLNAFTRDDL KAHLISLGAK VSGSVSKKTD
FLIAGENPGS KAQKAEKSGI KIMNEPELIE FLKALKPEGT KV
