ID S6BF36_PSERE Unreviewed; 790 AA.
AC S6BF36;
DT 16-OCT-2013, integrated into UniProtKB/TrEMBL.
DT 16-OCT-2013, sequence version 1.
DT 24-JAN-2024, entry version 59.
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 ECO:0000313|EMBL:BAN47669.1};
GN ORFNames=PCA10_19370 {ECO:0000313|EMBL:BAN47669.1};
OS Pseudomonas resinovorans NBRC 106553.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=1245471 {ECO:0000313|EMBL:BAN47669.1, ECO:0000313|Proteomes:UP000015503};
RN [1] {ECO:0000313|EMBL:BAN47669.1, ECO:0000313|Proteomes:UP000015503}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=NBRC 106553 {ECO:0000313|EMBL:BAN47669.1,
RC ECO:0000313|Proteomes:UP000015503};
RX PubMed=23887915; DOI=10.1128/genomeA.00488-13;
RA Shintani M., Hosoyama A., Ohji S., Tsuchikane K., Takarada H., Yamazoe A.,
RA Fujita N., Nojiri H.;
RT "Complete Genome Sequence of the Carbazole Degrader Pseudomonas
RT resinovorans Strain CA10 (NBRC 106553).";
RL Genome Announc. 1:e00488-13(2013).
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}.
CC -!- CAUTION: Lacks conserved residue(s) required for the propagation of
CC feature annotation. {ECO:0000256|HAMAP-Rule:MF_01588}.
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DR EMBL; AP013068; BAN47669.1; -; Genomic_DNA.
DR RefSeq; WP_016491869.1; NC_021499.1.
DR AlphaFoldDB; S6BF36; -.
DR STRING; 1245471.PCA10_19370; -.
DR KEGG; pre:PCA10_19370; -.
DR PATRIC; fig|1245471.3.peg.1966; -.
DR eggNOG; COG0272; Bacteria.
DR HOGENOM; CLU_007764_2_1_6; -.
DR OrthoDB; 9759736at2; -.
DR Proteomes; UP000015503; 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; 3.
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 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; PF12826; HHH_2; 2.
DR Pfam; PF14520; HHH_5; 1.
DR PIRSF; PIRSF001604; LigA; 2.
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; 2.
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:UP000015503};
KW Zinc {ECO:0000256|ARBA:ARBA00022833, ECO:0000256|HAMAP-Rule:MF_01588}.
FT DOMAIN 707..777
FT /note="BRCT"
FT /evidence="ECO:0000259|PROSITE:PS50172"
FT ACT_SITE 126
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 35..39
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 84..85
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 124
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 147
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 184
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 300
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 324
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 418
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 421
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 454
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
SQ SEQUENCE 790 AA; 85742 MW; 2AF304CAA9098C56 CRC64;
MTDAQTAANR IHALRAELDA HNHRYYVLDE PSVPDAEYDR LFRELQALEA EHPELVTPES
PTQRVGGEAL SEFGEVRHEV PMLSLGNAFE EEDLRAFDRS VQGGLGLSAG DLFGGGAEVE
YSCEPKLDGL AVSLLYRNGQ LVRGATRGDG STGEDISSNV RTIRNVPLKL QGEGWPELLE
VRGEVYMPKA GFDELNVRQA ESGGKTFANP RNAAAGSLRQ LDPKITASRP LEFCCYGVGQ
VSGELPATQV GMLQQLKAWG VPISRELKLA KGVEQCLAYY RDIGERRMDL PYDIDGVVFK
VNNIEDQQQL GFRARTPHWA LAHKFPAQEE LTELLDVEFQ VGRTGAVTPV ARLKPVKVAG
VTVANATLHN MDEVARLGLM IGDTVIIRRA GDVIPQVMQV VAERRPADAR PVHIPEQCPV
CGSAVERTQL VKRSKGKATT SEGSVYRCVG RLACAAQLKQ AIIHFASRRA LDIEGLGDKI
VEQLVDTGLV ASPADLFTLA YDQVVALEGF ADLSTRNLIN AIKDSSKPTL ARFIYALGIP
DVGEETAKVL ARALGSLARI RKALPEVLTY LPDVGLEVAS EIHNFFADEH NQQVIEALLA
RGLSLQEEGD LNPEFAACAT LPGFIDKLNI PFIAATGAEK LAAKFGTLEG IIKADWLDLR
QVERLNEKAA KSLRDFFDNP ANAQRAALIE AQLREFGMHW ESEKKTIEGL PLAGQTWVLT
GTLELMSRDV AKEKLEALGA KVAGSVSART HCVVAGPGAG SKLAKANELG VRVLDEEAFL
VELKGLGVAL
//
