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Database: UniProt
Entry: A0A411PDS4_9GAMM
LinkDB: A0A411PDS4_9GAMM
Original site: A0A411PDS4_9GAMM 
ID   A0A411PDS4_9GAMM        Unreviewed;       670 AA.
AC   A0A411PDS4;
DT   08-MAY-2019, integrated into UniProtKB/TrEMBL.
DT   08-MAY-2019, sequence version 1.
DT   24-JAN-2024, entry version 21.
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:QBF81612.1};
GN   ORFNames=EXU30_02065 {ECO:0000313|EMBL:QBF81612.1};
OS   Shewanella maritima.
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Alteromonadales;
OC   Shewanellaceae; Shewanella.
OX   NCBI_TaxID=2520507 {ECO:0000313|EMBL:QBF81612.1, ECO:0000313|Proteomes:UP000291106};
RN   [1] {ECO:0000313|EMBL:QBF81612.1, ECO:0000313|Proteomes:UP000291106}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=D4-2 {ECO:0000313|EMBL:QBF81612.1,
RC   ECO:0000313|Proteomes:UP000291106};
RA   Baek K.;
RT   "Shewanella sp. D4-2 isolated from Dokdo Island.";
RL   Submitted (FEB-2019) to the EMBL/GenBank/DDBJ databases.
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}.
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; CP036200; QBF81612.1; -; Genomic_DNA.
DR   AlphaFoldDB; A0A411PDS4; -.
DR   KEGG; smai:EXU30_02065; -.
DR   OrthoDB; 9759736at2; -.
DR   Proteomes; UP000291106; 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   Pfam; PF14520; HHH_5; 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   Zinc {ECO:0000256|ARBA:ARBA00022833, ECO:0000256|HAMAP-Rule:MF_01588}.
FT   DOMAIN          590..670
FT                   /note="BRCT"
FT                   /evidence="ECO:0000259|PROSITE:PS50172"
FT   ACT_SITE        112
FT                   /note="N6-AMP-lysine intermediate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         32..36
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         81..82
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         110
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         133
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         170
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         289
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         313
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         407
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         410
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         431
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
SQ   SEQUENCE   670 AA;  73281 MW;  91689212873E9327 CRC64;
     MQDIQSQMAQ LTETINQHNI RYYVDDAPSI PDAEYDRLMQ QLIALESEHP ELKLADSPTQ
     RVGGAPLDKF EQITHLKPML SLDNAFDQDD FEAFNKRITD KVSDVHYVCE PKLDGLAVSI
     TYRNGVLERA ATRGDGTVGE DITENVRTIR SIPLKLRGDD YPELVEVRGE VFMPKSAFDA
     LNARQLAKNE KVFVNPRNAA AGSLRQLDSK VAAERALDFY AYALGVVDGA SEPMSNEHYG
     QLMQLKKWGH PVSSEVKVCE SLTQVFDYYG DILNRRSELE YEIDGVVIKV NDITKQESLG
     FVAKAPRWAI AYKFPAQEEL TVLEAVDFQV GRTGAITPVA RLKPVFVGGV TVSNATLHNA
     DEIARLGVKV KDTVIIRRAG DVIPQIVAIV PEKRPEDAVD VSFPSQCPVC GSDAEREEGE
     AVLRCTGGLF CEAQRKEAIK HFASRKALNV DGLGDKVVEQ MIDKELIKSP ADLFALTPSM
     LTMLERMGMK SATKLVAAID SAKQTTLARF LYSLGIREVG EATAANLASH FKSLDAIKQA
     SLDQLIEVED VGAIVAKHIS HFFKQEHNVE VVDALIAAGV NWPAIEEVNE ADLSLKGQTW
     VLTGTLTQLN RNEAKAQLQA LGAKVAGSVS KNTDCLVAGE AAGSKLTKAQ DLGIKVIDEQ
     ALLDLLNSAG
//
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