DNLJ_HYDS0
ID DNLJ_HYDS0 Reviewed; 700 AA.
AC B4U8X0;
DT 28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT 23-SEP-2008, sequence version 1.
DT 03-AUG-2022, entry version 80.
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};
GN OrderedLocusNames=HY04AAS1_0894;
OS Hydrogenobaculum sp. (strain Y04AAS1).
OC Bacteria; Aquificae; Aquificales; Aquificaceae; Hydrogenobaculum;
OC unclassified Hydrogenobaculum.
OX NCBI_TaxID=380749;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Y04AAS1;
RX PubMed=19136599; DOI=10.1128/jb.01645-08;
RA Reysenbach A.-L., Hamamura N., Podar M., Griffiths E., Ferreira S.,
RA Hochstein R., Heidelberg J., Johnson J., Mead D., Pohorille A.,
RA Sarmiento M., Schweighofer K., Seshadri R., Voytek M.A.;
RT "Complete and draft genome sequences of six members of the Aquificales.";
RL J. Bacteriol. 191:1992-1993(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; CP001130; ACG57581.1; -; Genomic_DNA.
DR RefSeq; WP_012513937.1; NC_011126.1.
DR AlphaFoldDB; B4U8X0; -.
DR SMR; B4U8X0; -.
DR STRING; 380749.HY04AAS1_0894; -.
DR EnsemblBacteria; ACG57581; ACG57581; HY04AAS1_0894.
DR KEGG; hya:HY04AAS1_0894; -.
DR eggNOG; COG0272; Bacteria.
DR HOGENOM; CLU_007764_2_1_0; -.
DR OMA; HDVEHEI; -.
DR OrthoDB; 241401at2; -.
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; 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; 3.
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.
PE 3: Inferred from homology;
KW DNA damage; DNA repair; DNA replication; Ligase; Magnesium; Manganese;
KW Metal-binding; NAD; Zinc.
FT CHAIN 1..700
FT /note="DNA ligase"
FT /id="PRO_0000380400"
FT DOMAIN 619..700
FT /note="BRCT"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT ACT_SITE 143
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 61..65
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 110..111
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 141
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 164
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 202
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 321
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 345
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 439
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 442
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 457
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 462
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
SQ SEQUENCE 700 AA; 79140 MW; 12518ACD1B95593F CRC64;
MNDKFFIDKT KEILKTYNLS PDKHPPKLSK EEAIKIINTL RELINYHDYR YYVLNQPVIS
DAEYDAIYKF LKSIEDNYPD LITPDSLTQR VSSDISSTFP QVKHLAPMLS LDNTYNEDDL
RDFDRRVKEL SGKEHIEYCV EPKYDGAGIS LLYENDLFVR GATRGDGEVG EDVTKNLKTI
KTIPLRANFS KQGIRLLEIR GEVIINKDDF KKINEERMAE NLPPYANPRN LAAGSIRLQD
PQEVVKRPLT ALVYQITYVE PTNNMPKTHY GAIKMLHDLG FKTPFLDMKL CKNIQEVIDY
CRYFESKRES LPYEIDGMVI KVNDISLYDE LGFTSHAPRW ATAFKFKAKQ ATTIILDVIF
SVGRVGNITP VAKLEPVSLG GVTISSVSLF NEDFIREKDI HIKDTVIIER AGEVIPYVVS
VVKEARPKDA KPIVFPKYCP SCGSKLVKAP GEVAWRCINI SCPAQVVLRI RHFASKDAMD
IKGLGEAVAQ LLYDAKLVKN IADIYYLKFS DLVRLPRFAK KSAQNLIDAI EASKRRGLAR
VLYGLGIRYV GLTTAKKLAS YYKDIWNIVK ASEEDLRNIE DIGDIVARSI KEFFGLEQNI
NTIKRLEEAG VLLKEVSEAV SNKLAGLQFV FTGTLSCCTR EVARQMVESL GATTSDSVTH
HTSYLVVGQD PGATKLRKAN MLGIKTISEE EFLRLLEDSK
