DNLJ_HAEIN
ID DNLJ_HAEIN Reviewed; 670 AA.
AC P43813;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 15-JAN-2008, sequence version 2.
DT 03-AUG-2022, entry version 140.
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}; Synonyms=lig, ligN;
GN OrderedLocusNames=HI_1100;
OS Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pasteurellales;
OC Pasteurellaceae; Haemophilus.
OX NCBI_TaxID=71421;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 51907 / DSM 11121 / KW20 / Rd;
RX PubMed=7542800; DOI=10.1126/science.7542800;
RA Fleischmann R.D., Adams M.D., White O., Clayton R.A., Kirkness E.F.,
RA Kerlavage A.R., Bult C.J., Tomb J.-F., Dougherty B.A., Merrick J.M.,
RA McKenney K., Sutton G.G., FitzHugh W., Fields C.A., Gocayne J.D.,
RA Scott J.D., Shirley R., Liu L.-I., Glodek A., Kelley J.M., Weidman J.F.,
RA Phillips C.A., Spriggs T., Hedblom E., Cotton M.D., Utterback T.R.,
RA Hanna M.C., Nguyen D.T., Saudek D.M., Brandon R.C., Fine L.D.,
RA Fritchman J.L., Fuhrmann J.L., Geoghagen N.S.M., Gnehm C.L., McDonald L.A.,
RA Small K.V., Fraser C.M., Smith H.O., Venter J.C.;
RT "Whole-genome random sequencing and assembly of Haemophilus influenzae
RT Rd.";
RL Science 269:496-512(1995).
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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAC22753.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; L42023; AAC22753.1; ALT_INIT; Genomic_DNA.
DR PIR; D64182; D64182.
DR RefSeq; NP_439257.2; NC_000907.1.
DR RefSeq; WP_005665886.1; NC_000907.1.
DR PDB; 3BAC; X-ray; 3.00 A; A=64-327.
DR PDB; 3PN1; X-ray; 2.00 A; A=1-318.
DR PDB; 3UQ8; X-ray; 1.70 A; A=3-324.
DR PDB; 4UCO; X-ray; 2.50 A; A=1-324.
DR PDB; 4UCR; X-ray; 2.15 A; A=1-324.
DR PDB; 4UCS; X-ray; 1.90 A; A=1-324.
DR PDB; 4UCT; X-ray; 2.10 A; A=1-324.
DR PDB; 4UCU; X-ray; 2.10 A; A=1-324.
DR PDB; 4UCV; X-ray; 2.60 A; A=1-324.
DR PDB; 4UFZ; X-ray; 2.33 A; A=1-324.
DR PDBsum; 3BAC; -.
DR PDBsum; 3PN1; -.
DR PDBsum; 3UQ8; -.
DR PDBsum; 4UCO; -.
DR PDBsum; 4UCR; -.
DR PDBsum; 4UCS; -.
DR PDBsum; 4UCT; -.
DR PDBsum; 4UCU; -.
DR PDBsum; 4UCV; -.
DR PDBsum; 4UFZ; -.
DR AlphaFoldDB; P43813; -.
DR SMR; P43813; -.
DR STRING; 71421.HI_1100; -.
DR DrugBank; DB07041; N-[2-(2,4-diaminopyrido[2,3-d]pyrimidin-7-yl)-2-methylpropyl]-4-phenoxybenzamide.
DR EnsemblBacteria; AAC22753; AAC22753; HI_1100.
DR KEGG; hin:HI_1100; -.
DR PATRIC; fig|71421.8.peg.1146; -.
DR eggNOG; COG0272; Bacteria.
DR HOGENOM; CLU_007764_2_1_6; -.
DR PhylomeDB; P43813; -.
DR BioCyc; HINF71421:G1GJ1-1135-MON; -.
DR BRENDA; 6.5.1.2; 2529.
DR EvolutionaryTrace; P43813; -.
DR Proteomes; UP000000579; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0003911; F:DNA ligase (NAD+) activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006288; P:base-excision repair, DNA ligation; IBA:GO_Central.
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; 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; 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 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..670
FT /note="DNA ligase"
FT /id="PRO_0000161746"
FT DOMAIN 592..670
FT /note="BRCT"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT ACT_SITE 116
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 114
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 137
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 174
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 291
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 315
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
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 433
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT HELIX 4..23
FT /evidence="ECO:0007829|PDB:3UQ8"
FT HELIX 32..48
FT /evidence="ECO:0007829|PDB:3UQ8"
FT HELIX 50..52
FT /evidence="ECO:0007829|PDB:3UQ8"
FT HELIX 58..60
FT /evidence="ECO:0007829|PDB:3UQ8"
FT STRAND 72..74
FT /evidence="ECO:0007829|PDB:3UQ8"
FT HELIX 88..101
FT /evidence="ECO:0007829|PDB:3UQ8"
FT STRAND 102..104
FT /evidence="ECO:0007829|PDB:4UCS"
FT STRAND 110..127
FT /evidence="ECO:0007829|PDB:3UQ8"
FT STRAND 130..136
FT /evidence="ECO:0007829|PDB:3UQ8"
FT STRAND 140..145
FT /evidence="ECO:0007829|PDB:3UQ8"
FT HELIX 147..151
FT /evidence="ECO:0007829|PDB:3UQ8"
FT STRAND 161..164
FT /evidence="ECO:0007829|PDB:4UCS"
FT STRAND 167..176
FT /evidence="ECO:0007829|PDB:3UQ8"
FT HELIX 179..191
FT /evidence="ECO:0007829|PDB:3UQ8"
FT HELIX 200..208
FT /evidence="ECO:0007829|PDB:3UQ8"
FT HELIX 213..216
FT /evidence="ECO:0007829|PDB:3UQ8"
FT STRAND 222..233
FT /evidence="ECO:0007829|PDB:3UQ8"
FT HELIX 240..249
FT /evidence="ECO:0007829|PDB:3UQ8"
FT STRAND 259..263
FT /evidence="ECO:0007829|PDB:3UQ8"
FT HELIX 264..276
FT /evidence="ECO:0007829|PDB:3UQ8"
FT TURN 277..281
FT /evidence="ECO:0007829|PDB:3UQ8"
FT STRAND 285..294
FT /evidence="ECO:0007829|PDB:3UQ8"
FT HELIX 295..301
FT /evidence="ECO:0007829|PDB:3UQ8"
FT STRAND 311..315
FT /evidence="ECO:0007829|PDB:3UQ8"
FT HELIX 319..321
FT /evidence="ECO:0007829|PDB:3UQ8"
SQ SEQUENCE 670 AA; 74043 MW; A4110EE380A76C9C CRC64;
MTNIQTQLDN LRKTLRQYEY EYHVLDNPSV PDSEYDRLFH QLKALELEHP EFLTSDSPTQ
RVGAKPLSGF SQIRHEIPML SLDNAFSDAE FNAFVKRIED RLILLPKPLT FCCEPKLDGL
AVSILYVNGE LTQAATRGDG TTGEDITANI RTIRNVPLQL LTDNPPARLE VRGEVFMPHA
GFERLNKYAL EHNEKTFANP RNAAAGSLRQ LDPNITSKRP LVLNAYGIGI AEGVDLPTTH
YARLQWLKSI GIPVNPEIRL CNGADEVLGF YRDIQNKRSS LGYDIDGTVL KINDIALQNE
LGFISKAPRW AIAYKFPAQE ELTLLNDVEF QVGRTGAITP VAKLEPVFVA GVTVSNATLH
NGDEIERLNI AIGDTVVIRR AGDVIPQIIG VLHERRPDNA KPIIFPTNCP VCDSQIIRIE
GEAVARCTGG LFCAAQRKEA LKHFVSRKAM DIDGVGGKLI EQLVDRELIH TPADLFKLDL
TTLTRLERMG AKSAENALNS LENAKSTTLA RFIFALGIRE VGEATALNLA NHFKTLDALK
DANLEELQQV PDVGEVVANR IFIFWREAHN VAVVEDLIAQ GVHWETVEVK EASENLFKDK
TVVLTGTLTQ MGRNEAKALL QQLGAKVSGS VSSKTDFVIA GDAAGSKLAK AQELNITVLT
EEEFLAQITR
