ID C7QYX3_JONDD Unreviewed; 798 AA.
AC C7QYX3;
DT 13-OCT-2009, integrated into UniProtKB/TrEMBL.
DT 13-OCT-2009, sequence version 1.
DT 27-MAR-2024, entry version 89.
DE RecName: Full=DNA ligase {ECO:0000256|HAMAP-Rule:MF_01588, ECO:0000256|RuleBase:RU000618};
DE EC=6.5.1.2 {ECO:0000256|HAMAP-Rule:MF_01588, ECO:0000256|RuleBase:RU000618};
DE AltName: Full=Polydeoxyribonucleotide synthase [NAD(+)] {ECO:0000256|HAMAP-Rule:MF_01588};
GN Name=ligA {ECO:0000256|HAMAP-Rule:MF_01588};
GN OrderedLocusNames=Jden_1716 {ECO:0000313|EMBL:ACV09362.1};
OS Jonesia denitrificans (strain ATCC 14870 / DSM 20603 / BCRC 15368 / CIP
OS 55.134 / JCM 11481 / NBRC 15587 / NCTC 10816 / Prevot 55134) (Listeria
OS denitrificans).
OC Bacteria; Actinomycetota; Actinomycetes; Micrococcales; Jonesiaceae;
OC Jonesia.
OX NCBI_TaxID=471856 {ECO:0000313|EMBL:ACV09362.1, ECO:0000313|Proteomes:UP000000628};
RN [1] {ECO:0000313|EMBL:ACV09362.1, ECO:0000313|Proteomes:UP000000628}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 14870 / DSM 20603 / BCRC 15368 / CIP 55.134 / JCM 11481 /
RC NBRC 15587 / NCTC 10816 / Prevot 55134
RC {ECO:0000313|Proteomes:UP000000628};
RX PubMed=21304666; DOI=10.4056/sigs.41646;
RA Pukall R., Gehrich-Schroter G., Lapidus A., Nolan M., Glavina Del Rio T.,
RA Lucas S., Chen F., Tice H., Pitluck S., Cheng J.F., Copeland A.,
RA Saunders E., Brettin T., Detter J.C., Bruce D., Goodwin L., Pati A.,
RA Ivanova N., Mavromatis K., Ovchinnikova G., Chen A., Palaniappan K.,
RA Land M., Hauser L., Chang Y.J., Jeffries C.D., Chain P., Goker M.,
RA Bristow J., Eisen J.A., Markowitz V., Hugenholtz P., Kyrpides N.C.,
RA Klenk H.P., Han C.;
RT "Complete genome sequence of Jonesia denitrificans type strain (Prevot
RT 55134).";
RL Stand. Genomic Sci. 1:262-269(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:0000256|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;
CC Evidence={ECO:0000256|ARBA:ARBA00034005, ECO:0000256|HAMAP-
CC Rule:MF_01588, ECO:0000256|RuleBase:RU000618};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01588};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01588};
CC -!- SIMILARITY: Belongs to the NAD-dependent DNA ligase family. LigA
CC subfamily. {ECO:0000256|HAMAP-Rule:MF_01588}.
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DR EMBL; CP001706; ACV09362.1; -; Genomic_DNA.
DR AlphaFoldDB; C7QYX3; -.
DR STRING; 471856.Jden_1716; -.
DR KEGG; jde:Jden_1716; -.
DR eggNOG; COG0272; Bacteria.
DR HOGENOM; CLU_007764_2_1_11; -.
DR Proteomes; UP000000628; 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; cd17748; BRCT_DNA_ligase_like; 1.
DR CDD; cd00114; LIGANc; 1.
DR Gene3D; 6.20.10.30; -; 1.
DR Gene3D; 1.10.150.20; 5' to 3' exonuclease, C-terminal subdomain; 2.
DR Gene3D; 3.40.50.10190; BRCT domain; 1.
DR Gene3D; 3.30.470.30; DNA ligase/mRNA capping enzyme; 1.
DR Gene3D; 1.10.287.610; Helix hairpin bin; 1.
DR Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 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; DNA_ligase.
DR InterPro; IPR018239; DNA_ligase_AS.
DR InterPro; IPR033136; DNA_ligase_CS.
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 NCBIfam; TIGR00575; dnlj; 1.
DR PANTHER; PTHR23389; CHROMOSOME TRANSMISSION FIDELITY FACTOR 18; 1.
DR PANTHER; PTHR23389:SF9; DNA LIGASE; 1.
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; SSF52113; BRCT domain; 1.
DR SUPFAM; SSF56091; DNA ligase/mRNA capping enzyme, catalytic domain; 1.
DR SUPFAM; SSF50249; Nucleic acid-binding proteins; 1.
DR SUPFAM; SSF47781; RuvA domain 2-like; 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 {ECO:0000256|ARBA:ARBA00022763, ECO:0000256|HAMAP-
KW Rule:MF_01588};
KW DNA repair {ECO:0000256|ARBA:ARBA00023204, ECO:0000256|HAMAP-
KW Rule:MF_01588};
KW DNA replication {ECO:0000256|ARBA:ARBA00022705, ECO:0000256|HAMAP-
KW Rule:MF_01588};
KW Ligase {ECO:0000256|ARBA:ARBA00022598, ECO:0000256|HAMAP-Rule:MF_01588};
KW Magnesium {ECO:0000256|ARBA:ARBA00022842, ECO:0000256|HAMAP-Rule:MF_01588};
KW Manganese {ECO:0000256|HAMAP-Rule:MF_01588};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_01588};
KW NAD {ECO:0000256|ARBA:ARBA00023027, ECO:0000256|HAMAP-Rule:MF_01588};
KW Reference proteome {ECO:0000313|Proteomes:UP000000628};
KW Zinc {ECO:0000256|ARBA:ARBA00022833, ECO:0000256|HAMAP-Rule:MF_01588}.
FT DOMAIN 701..771
FT /note="BRCT"
FT /evidence="ECO:0000259|PROSITE:PS50172"
FT REGION 1..29
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 239..259
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 8..26
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 162
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 81..85
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 129..130
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 160
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 183
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 222
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 343
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 367
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 461
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 464
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 480
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 486
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
SQ SEQUENCE 798 AA; 86912 MW; 74A98B5D4130A1CD CRC64;
MARACQWSVD NSEVTTNDQN AHDSSLARPF TGPEVAAGSA AARIVDAAAE VSLQEQWERL
ARLIQRYQFE YYIQGESSVP DADYDALLAE LVAVEEQLGG APQGSPTQRV GGTFSTEFEE
VDHRQPMLSL DNAFSLEELQ AWADRVHGEL SGGAVSYLCE VKIDGLAVSL TYERGELVRA
LTRGDGQTGE DVTLNVQTIR SIPQRLGGDP AFHPQVVEIR GEVFMKVADF ADLNDSQARQ
GGKTFANPRN AAAGSLRQKD PRVTAQRRLS MYAHGIGALE WDGQSPVDLA RQSDVYALYQ
QWGIPVSSHN SVEHDLDAVT RKIEYYRENR HSIEHELDGF VIKVDEVAAQ KQLGSTSRAP
RWAIAFKYPP EEVTTRLLDI QVNVGRTGRV TPFGMMEPVL VAGSTVSMAT LHNFHEVRRK
DVRPGDTVIV RKAGDVIPEI LGAVESLRPD GLPQWEPPTH CPSCGTEIRE AKEGDKDLRC
PNAQSCPSQL RERVFALASR GAFDIEALGW ESAVALCDPE SSRPVGPDAP QLDGPPLTPV
LTSEAHIFDL ADENSSLTRS LKDVVVWRER KLKSGTRWEL VPYFYTRATA SKSSVPTATT
VKLFEEVQKA KSQPLWRVLV ALSIRHVGPT AARALATEFG SMDRIRAASV SELAAVDGVG
STIAESVVEW FREVDGNQWR PAIVAAWAKA GVSMEDIPDE SVQRTLEGIT VVVTGGLENF
TRDGVKEAIV ARGGKASGSV SKKTDFVVVG ANAGSKETKA RELGLRILNE EEFTRLLAGG
PDAVNASHSS ESVSEVSD
//
