DNLJ_HALVD
ID DNLJ_HALVD Reviewed; 699 AA.
AC D4GY98;
DT 29-OCT-2014, integrated into UniProtKB/Swiss-Prot.
DT 18-MAY-2010, sequence version 1.
DT 03-AUG-2022, entry version 77.
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=ligN {ECO:0000303|PubMed:16420348};
GN Synonyms=ligA {ECO:0000255|HAMAP-Rule:MF_01588};
GN OrderedLocusNames=HVO_3000 {ECO:0000312|EMBL:ADE03170.1};
GN ORFNames=C498_18165 {ECO:0000312|EMBL:ELY24606.1};
OS Haloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 /
OS NCIMB 2012 / VKM B-1768 / DS2) (Halobacterium volcanii).
OC Archaea; Euryarchaeota; Stenosarchaea group; Halobacteria; Haloferacales;
OC Haloferacaceae; Haloferax.
OX NCBI_TaxID=309800;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM
RC B-1768 / DS2;
RX PubMed=20333302; DOI=10.1371/journal.pone.0009605;
RA Hartman A.L., Norais C., Badger J.H., Delmas S., Haldenby S., Madupu R.,
RA Robinson J., Khouri H., Ren Q., Lowe T.M., Maupin-Furlow J.,
RA Pohlschroder M., Daniels C., Pfeiffer F., Allers T., Eisen J.A.;
RT "The complete genome sequence of Haloferax volcanii DS2, a model
RT archaeon.";
RL PLoS ONE 5:E9605-E9605(2010).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM
RC B-1768 / DS2;
RX PubMed=25393412; DOI=10.1371/journal.pgen.1004784;
RA Becker E.A., Seitzer P.M., Tritt A., Larsen D., Krusor M., Yao A.I., Wu D.,
RA Madern D., Eisen J.A., Darling A.E., Facciotti M.T.;
RT "Phylogenetically driven sequencing of extremely halophilic archaea reveals
RT strategies for static and dynamic osmo-response.";
RL PLoS Genet. 10:E1004784-E1004784(2014).
RN [3]
RP DISRUPTION PHENOTYPE, AND GENE NAME.
RX PubMed=16420348; DOI=10.1111/j.1365-2958.2005.04975.x;
RA Zhao A., Gray F.C., MacNeill S.A.;
RT "ATP- and NAD+-dependent DNA ligases share an essential function in the
RT halophilic archaeon Haloferax volcanii.";
RL Mol. Microbiol. 59:743-752(2006).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ACTIVITY REGULATION, AND
RP MUTAGENESIS OF LYS-139 AND ASP-141.
RX PubMed=17132163; DOI=10.1186/1471-2199-7-44;
RA Poidevin L., MacNeill S.A.;
RT "Biochemical characterisation of LigN, an NAD+-dependent DNA ligase from
RT the halophilic euryarchaeon Haloferax volcanii that displays maximal in
RT vitro activity at high salt concentrations.";
RL BMC Mol. Biol. 7:44-44(2006).
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, ECO:0000269|PubMed:17132163}.
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, ECO:0000269|PubMed:17132163};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01588,
CC ECO:0000269|PubMed:17132163};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01588,
CC ECO:0000269|PubMed:17132163};
CC -!- ACTIVITY REGULATION: Displays maximal in vitro activity at high salt
CC levels. {ECO:0000269|PubMed:17132163}.
CC -!- DISRUPTION PHENOTYPE: Deletion of both ligA and ligN is lethal.
CC {ECO:0000269|PubMed:16420348}.
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; CP001956; ADE03170.1; -; Genomic_DNA.
DR EMBL; AOHU01000104; ELY24606.1; -; Genomic_DNA.
DR RefSeq; WP_004044909.1; NZ_AOHU01000104.1.
DR AlphaFoldDB; D4GY98; -.
DR SMR; D4GY98; -.
DR STRING; 309800.C498_18165; -.
DR EnsemblBacteria; ADE03170; ADE03170; HVO_3000.
DR EnsemblBacteria; ELY24606; ELY24606; C498_18165.
DR GeneID; 8923962; -.
DR KEGG; hvo:HVO_3000; -.
DR PATRIC; fig|309800.29.peg.3531; -.
DR eggNOG; arCOG04754; Archaea.
DR HOGENOM; CLU_007764_2_1_2; -.
DR OMA; HDVEHEI; -.
DR OrthoDB; 3788at2157; -.
DR Proteomes; UP000008243; Chromosome.
DR Proteomes; UP000011532; Unassembled WGS sequence.
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 Pfam; PF00533; BRCT; 1.
DR Pfam; PF01653; DNA_ligase_aden; 1.
DR Pfam; PF03120; DNA_ligase_OB; 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.
DR PROSITE; PS01055; DNA_LIGASE_N1; 1.
DR PROSITE; PS01056; DNA_LIGASE_N2; 1.
PE 1: Evidence at protein level;
KW DNA damage; DNA repair; DNA replication; Ligase; Magnesium; Manganese;
KW Metal-binding; NAD; Reference proteome; Zinc.
FT CHAIN 1..699
FT /note="DNA ligase"
FT /id="PRO_0000430565"
FT DOMAIN 613..666
FT /note="BRCT"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT REGION 1..29
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 139
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 60..64
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 108..109
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 160
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 196
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 311
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 335
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 425
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 428
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 441
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 447
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT MUTAGEN 139
FT /note="K->A: Lack of activity."
FT /evidence="ECO:0000269|PubMed:17132163"
FT MUTAGEN 141
FT /note="D->A: Lack of activity."
FT /evidence="ECO:0000269|PubMed:17132163"
SQ SEQUENCE 699 AA; 75811 MW; 90C91BCDC29548CE CRC64;
MSDADVDAES NPYLRDPPTE FEPAESLSRE AAEGQAALLR EAVREHDHRY YVAADPLVSD
AAYDALFSRL VALEDAFDLD TTNSPTNRVG GEPIDALETV EHVAPMLSID QSTDADDLRE
FDERVRREVG AVDYVCEPKF DGLSVEVVYE DGEFVRAATR GDGRRGDDVS AQVKTIPTVP
LSLRGDHPDR LAVRGEIYMP KSDFSDLNAR RVEAGEDAFA NPRNAAAGTL RNLDPSVVAD
RPLAVFFYDI LDASARPDSQ WAALDRLREW GLRVTDRIER AEDVAEAIDY RDRMQAARDD
LDYEIDGTVI KVDSRDARER LGEKSRSVRW AFAYKFPARH EVTTVRDIVV QVGRTGRLTP
VAILDPVDVG GVTVSRATLH NPDERAALGV AVGDRVRVKR AGDVIPQVVE VTEDGGGCYE
FPDECPVCGS AVDRDGPLAF CSGGLSCPAQ REASIGHFAV KGAMDIDGLG EERVAQLVDA
GLVETVADLY DLTADDLAEL EGWGETSAEN LVAAVENAKH PSLDSFLVGL SIPEVGEATA
RGLAREFGSI EAFPIEADAE EDEFDAFEER LTTVPDVGET VARRVRDFFE NADNRAVIRA
LLDRGVDPEP VESGGDELDG LTFVVTGTLA ASRSDVTELV ESHGGNVTGS VSGNTDYLVV
GENPGRSKRD DAEANDVPTL AETEFEALLA ERGVAYPPE
