DNLJ_ENTFA
ID DNLJ_ENTFA Reviewed; 676 AA.
AC Q837V6;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 129.
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=EF_0722;
OS Enterococcus faecalis (strain ATCC 700802 / V583).
OC Bacteria; Firmicutes; Bacilli; Lactobacillales; Enterococcaceae;
OC Enterococcus.
OX NCBI_TaxID=226185;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700802 / V583;
RX PubMed=12663927; DOI=10.1126/science.1080613;
RA Paulsen I.T., Banerjei L., Myers G.S.A., Nelson K.E., Seshadri R.,
RA Read T.D., Fouts D.E., Eisen J.A., Gill S.R., Heidelberg J.F., Tettelin H.,
RA Dodson R.J., Umayam L.A., Brinkac L.M., Beanan M.J., Daugherty S.C.,
RA DeBoy R.T., Durkin S.A., Kolonay J.F., Madupu R., Nelson W.C.,
RA Vamathevan J.J., Tran B., Upton J., Hansen T., Shetty J., Khouri H.M.,
RA Utterback T.R., Radune D., Ketchum K.A., Dougherty B.A., Fraser C.M.;
RT "Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus
RT faecalis.";
RL Science 299:2071-2074(2003).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 1-325 IN COMPLEXES WITH NAD AND
RP NICOTINAMIDE NUCLEOTIDE.
RX PubMed=15296738; DOI=10.1016/j.str.2004.05.017;
RA Gajiwala K.S., Pinko C.;
RT "Structural rearrangement accompanying NAD+ synthesis within a bacterial
RT DNA ligase crystal.";
RL Structure 12:1449-1459(2004).
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; AE016830; AAO80542.1; -; Genomic_DNA.
DR RefSeq; NP_814472.1; NC_004668.1.
DR RefSeq; WP_002361258.1; NZ_KE136527.1.
DR PDB; 1TA8; X-ray; 1.80 A; A=1-323.
DR PDB; 1TAE; X-ray; 2.70 A; A/B/C/D=1-324.
DR PDB; 3BA8; X-ray; 1.90 A; A=1-324.
DR PDB; 3BA9; X-ray; 1.90 A; A=1-324.
DR PDB; 3BAA; X-ray; 1.90 A; A=1-324.
DR PDB; 3BAB; X-ray; 2.50 A; A=1-324.
DR PDB; 4EEQ; X-ray; 2.10 A; A=1-323.
DR PDB; 4EFB; X-ray; 2.20 A; A=1-323.
DR PDB; 4EFE; X-ray; 2.00 A; A=1-323.
DR PDB; 4LH6; X-ray; 1.65 A; A=1-323.
DR PDB; 4LH7; X-ray; 1.90 A; A=1-323.
DR PDBsum; 1TA8; -.
DR PDBsum; 1TAE; -.
DR PDBsum; 3BA8; -.
DR PDBsum; 3BA9; -.
DR PDBsum; 3BAA; -.
DR PDBsum; 3BAB; -.
DR PDBsum; 4EEQ; -.
DR PDBsum; 4EFB; -.
DR PDBsum; 4EFE; -.
DR PDBsum; 4LH6; -.
DR PDBsum; 4LH7; -.
DR AlphaFoldDB; Q837V6; -.
DR SMR; Q837V6; -.
DR STRING; 226185.EF_0722; -.
DR DrugBank; DB07040; 2-amino-7-fluoro-5-oxo-5H-chromeno[2,3-b]pyridine-3-carboxamide.
DR DrugBank; DB07043; 7-amino-2-tert-butyl-4-(4-pyrimidin-2-ylpiperazin-1-yl)pyrido[2,3-d]pyrimidine-6-carboxamide.
DR DrugBank; DB07042; 7-amino-2-tert-butyl-4-{[2-(1H-imidazol-4-yl)ethyl]amino}pyrido[2,3-d]pyrimidine-6-carboxamide.
DR DrugBank; DB07041; N-[2-(2,4-diaminopyrido[2,3-d]pyrimidin-7-yl)-2-methylpropyl]-4-phenoxybenzamide.
DR DrugBank; DB03227; Nicotinamide Mononucleotide.
DR EnsemblBacteria; AAO80542; AAO80542; EF_0722.
DR KEGG; efa:EF0722; -.
DR PATRIC; fig|226185.9.peg.667; -.
DR eggNOG; COG0272; Bacteria.
DR HOGENOM; CLU_007764_2_1_9; -.
DR OMA; HDVEHEI; -.
DR BRENDA; 6.5.1.2; 2095.
DR EvolutionaryTrace; Q837V6; -.
DR Proteomes; UP000001415; Chromosome.
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; 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; 1.
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; 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 1: Evidence at protein level;
KW 3D-structure; DNA damage; DNA repair; DNA replication; Ligase; Magnesium;
KW Manganese; Metal-binding; NAD; Reference proteome; Zinc.
FT CHAIN 1..676
FT /note="DNA ligase"
FT /id="PRO_0000313228"
FT DOMAIN 595..676
FT /note="BRCT"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT ACT_SITE 120
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 39..43
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588,
FT ECO:0000269|PubMed:15296738"
FT BINDING 88..91
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588,
FT ECO:0000269|PubMed:15296738"
FT BINDING 118
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588,
FT ECO:0000269|PubMed:15296738"
FT BINDING 141
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588,
FT ECO:0000269|PubMed:15296738"
FT BINDING 175
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588,
FT ECO:0000269|PubMed:15296738"
FT BINDING 291
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588,
FT ECO:0000269|PubMed:15296738"
FT BINDING 315
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588,
FT ECO:0000269|PubMed:15296738"
FT BINDING 409
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 412
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 427
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 432
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT HELIX 8..30
FT /evidence="ECO:0007829|PDB:4LH6"
FT STRAND 31..33
FT /evidence="ECO:0007829|PDB:1TAE"
FT HELIX 39..55
FT /evidence="ECO:0007829|PDB:4LH6"
FT HELIX 57..59
FT /evidence="ECO:0007829|PDB:4LH6"
FT HELIX 65..67
FT /evidence="ECO:0007829|PDB:4LH6"
FT STRAND 79..81
FT /evidence="ECO:0007829|PDB:4LH6"
FT HELIX 95..109
FT /evidence="ECO:0007829|PDB:4LH6"
FT STRAND 115..121
FT /evidence="ECO:0007829|PDB:4LH6"
FT STRAND 123..131
FT /evidence="ECO:0007829|PDB:4LH6"
FT STRAND 134..140
FT /evidence="ECO:0007829|PDB:4LH6"
FT STRAND 144..149
FT /evidence="ECO:0007829|PDB:4LH6"
FT HELIX 151..155
FT /evidence="ECO:0007829|PDB:4LH6"
FT STRAND 165..167
FT /evidence="ECO:0007829|PDB:1TAE"
FT STRAND 170..177
FT /evidence="ECO:0007829|PDB:4LH6"
FT HELIX 180..192
FT /evidence="ECO:0007829|PDB:4LH6"
FT HELIX 201..209
FT /evidence="ECO:0007829|PDB:4LH6"
FT HELIX 214..219
FT /evidence="ECO:0007829|PDB:4LH6"
FT STRAND 223..230
FT /evidence="ECO:0007829|PDB:4LH6"
FT HELIX 240..250
FT /evidence="ECO:0007829|PDB:4LH6"
FT STRAND 259..263
FT /evidence="ECO:0007829|PDB:4LH6"
FT HELIX 264..277
FT /evidence="ECO:0007829|PDB:4LH6"
FT HELIX 278..280
FT /evidence="ECO:0007829|PDB:4LH6"
FT STRAND 281..283
FT /evidence="ECO:0007829|PDB:1TA8"
FT STRAND 285..294
FT /evidence="ECO:0007829|PDB:4LH6"
FT HELIX 295..301
FT /evidence="ECO:0007829|PDB:4LH6"
FT STRAND 305..315
FT /evidence="ECO:0007829|PDB:4LH6"
FT HELIX 319..321
FT /evidence="ECO:0007829|PDB:4LH6"
SQ SEQUENCE 676 AA; 75584 MW; 9B6B93FD8DBB8E3B CRC64;
MEQQPLTLTA ATTRAQELRK QLNQYSHEYY VKDQPSVEDY VYDRLYKELV DIETEFPDLI
TPDSPTQRVG GKVLSGFEKA PHDIPMYSLN DGFSKEDIFA FDERVRKAIG KPVAYCCELK
IDGLAISLRY ENGVFVRGAT RGDGTVGENI TENLRTVRSV PMRLTEPISV EVRGECYMPK
QSFVALNEER EENGQDIFAN PRNAAAGSLR QLDTKIVAKR NLNTFLYTVA DFGPMKAKTQ
FEALEELSAI GFRTNPERQL CQSIDEVWAY IEEYHEKRST LPYEIDGIVI KVNEFALQDE
LGFTVKAPRW AIAYKFPPEE AETVVEDIEW TIGRTGVVTP TAVMAPVRVA GTTVSRASLH
NADFIQMKDI RLNDHVIIYK AGDIIPEVAQ VLVEKRAADS QPYEMPTHCP ICHSELVHLD
EEVALRCINP KCPAQIKEGL NHFVSRNAMN IDGLGPRVLA QMYDKGLVKD VADLYFLTEE
QLMTLDKIKE KSANNIYTAI QGSKENSVER LIFGLGIRHV GAKAAKILAE HFGDLPTLSR
ATAEEIVALD SIGETIADSV VTYFENEEVH ELMAELEKAQ VNLTYKGLRT EQLAEVESPF
KDKTVVLTGK LAQYTREEAK EKIENLGGKV TGSVSKKTDI VVAGEDAGSK LTKAESLGVT
VWNEQEMVDA LDASHF
