ID D5SRH3_PLAL2 Unreviewed; 707 AA.
AC D5SRH3;
DT 13-JUL-2010, integrated into UniProtKB/TrEMBL.
DT 13-JUL-2010, sequence version 1.
DT 27-MAR-2024, entry version 85.
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=Plim_2844 {ECO:0000313|EMBL:ADG68666.1};
OS Planctopirus limnophila (strain ATCC 43296 / DSM 3776 / IFAM 1008 / Mu 290)
OS (Planctomyces limnophilus).
OC Bacteria; Planctomycetota; Planctomycetia; Planctomycetales;
OC Planctomycetaceae; Planctopirus.
OX NCBI_TaxID=521674 {ECO:0000313|EMBL:ADG68666.1, ECO:0000313|Proteomes:UP000002220};
RN [1] {ECO:0000313|EMBL:ADG68666.1, ECO:0000313|Proteomes:UP000002220}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43296 / DSM 3776 / IFAM 1008 / 290
RC {ECO:0000313|Proteomes:UP000002220};
RX PubMed=21304691; DOI=10.4056/sigs.1052813;
RA Labutti K., Sikorski J., Schneider S., Nolan M., Lucas S.,
RA Glavina Del Rio T., Tice H., Cheng J.F., Goodwin L., Pitluck S.,
RA Liolios K., Ivanova N., Mavromatis K., Mikhailova N., Pati A., Chen A.,
RA Palaniappan K., Land M., Hauser L., Chang Y.J., Jeffries C.D.,
RA Tindall B.J., Rohde M., Goker M., Woyke T., Bristow J., Eisen J.A.,
RA Markowitz V., Hugenholtz P., Kyrpides N.C., Klenk H.P., Lapidus A.;
RT "Complete genome sequence of Planctomyces limnophilus type strain (Mu
RT 290).";
RL Stand. Genomic Sci. 3:47-56(2010).
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|ARBA:ARBA00004067, 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; CP001744; ADG68666.1; -; Genomic_DNA.
DR RefSeq; WP_013111097.1; NC_014148.1.
DR AlphaFoldDB; D5SRH3; -.
DR STRING; 521674.Plim_2844; -.
DR KEGG; plm:Plim_2844; -.
DR eggNOG; COG0272; Bacteria.
DR HOGENOM; CLU_007764_2_1_0; -.
DR Proteomes; UP000002220; Chromosome.
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; 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; 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 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 Pfam; PF14520; HHH_5; 1.
DR PIRSF; PIRSF001604; LigA; 1.
DR SMART; SM00292; BRCT; 1.
DR SMART; SM00278; HhH1; 4.
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:UP000002220};
KW Zinc {ECO:0000256|ARBA:ARBA00022833, ECO:0000256|HAMAP-Rule:MF_01588}.
FT DOMAIN 628..707
FT /note="BRCT"
FT /evidence="ECO:0000259|PROSITE:PS50172"
FT ACT_SITE 136
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 50..54
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 99..100
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 134
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 157
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 204
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 323
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 347
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 441
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 444
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 459
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"
SQ SEQUENCE 707 AA; 78225 MW; FF3151D81426D01C CRC64;
MWDSMSIAEL LARPLPTSAD QARHLLDKLR QEIRRHDRLY YVLAQNEISD LEYDRLMARL
LEVEAAFPEL TTADSPSQKV GGEPIEGFVQ VAHSVPMLSI DNVYDESGLL EFGQKVSRRA
SEVGWKGPME WLAEFKVDGV ALSLIYEEGK LIRAVTRGDG RVGDDVTHNA KTIKGVPLFL
EDGSSKKSLF AESNIPRLLE VRGEAYIGNQ DFAKVRAHQL ERGEEPFKNS RNATAGSLKL
LDPKLCAQRQ LRFFAHSLGA IDEQEATRFK THADYLELFY QVGLPTVPMT ACHPSFEAAV
AASPTMMEAL STLDFEVDGL VFKVNNLALR AELGMTSKSP RWIVAYKWER YEAATKVLNI
TVQVGKTGVL TPVADLEPVE IAGTTVSRSS LHNRDEIERL GLGVGDTVIV EKAGKIIPHI
VRVEEHLRPT NTAPYRFPET CPECSTIVEQ DEGGVYIRCP NINCPARFRE SLRYFASRQA
MDIEGLGTKL VEQLVSSRLV QSISDLYRLV DKRAELLELE RLGEKSVDSL LAGLEASRQQ
PLWRLLTALN IRHVGQRTAQ ILAERFGSMD RLSAQTIEEL SATPEVGEVI AQSVHHFFHT
EYGSKLIEEL KNLGLNLGTE SEQKQIAATE GVLSGKTFVV TGTLPSMGRE EIEELIRLHG
GHAASSVSKK TSFVVAGENA GSKLTKAQSL GVPVINEAEF MKLIGKA
//
