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DNA ligase (EC 6.5.1.2) (Polydeoxyribonucleotide synthase [NAD( )])

 F7XU39_MIDMI            Unreviewed;       675 AA.
F7XU39;
21-SEP-2011, integrated into UniProtKB/TrEMBL.
21-SEP-2011, sequence version 1.
07-JUN-2017, entry version 46.
RecName: Full=DNA ligase {ECO:0000256|HAMAP-Rule:MF_01588};
EC=6.5.1.2 {ECO:0000256|HAMAP-Rule:MF_01588};
AltName: Full=Polydeoxyribonucleotide synthase [NAD(+)] {ECO:0000256|HAMAP-Rule:MF_01588};
Name=lig {ECO:0000313|EMBL:AEI89398.1};
Synonyms=ligA {ECO:0000256|HAMAP-Rule:MF_01588};
OrderedLocusNames=midi_01121 {ECO:0000313|EMBL:AEI89398.1};
Midichloria mitochondrii (strain IricVA).
Bacteria; Proteobacteria; Alphaproteobacteria; Rickettsiales;
Candidatus Midichloriaceae; Candidatus Midichloria.
NCBI_TaxID=696127 {ECO:0000313|EMBL:AEI89398.1, ECO:0000313|Proteomes:UP000006639};
[1] {ECO:0000313|EMBL:AEI89398.1, ECO:0000313|Proteomes:UP000006639}
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=IricVA {ECO:0000313|EMBL:AEI89398.1,
ECO:0000313|Proteomes:UP000006639};
PubMed=21690562; DOI=10.1093/molbev/msr159;
Sassera D., Lo N., Epis S., D'Auria G., Montagna M., Comandatore F.,
Horner D., Pereto J., Luciano A.M., Franciosi F., Ferri E., Crotti E.,
Bazzocchi C., Daffonchio D., Sacchi L., Moya A., Latorre A., Bandi C.;
"Phylogenomic evidence for the presence of a flagellum and cbb3
oxidase in the free-living mitochondrial ancestor.";
Mol. Biol. Evol. 28:3285-3296(2011).
-!- FUNCTION: DNA ligase that catalyzes the formation of
phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl
groups in double-stranded DNA using NAD as a coenzyme and as the
energy source for the reaction. It is essential for DNA
replication and repair of damaged DNA. {ECO:0000256|HAMAP-
Rule:MF_01588, ECO:0000256|SAAS:SAAS00572229}.
-!- CATALYTIC ACTIVITY: NAD(+) + (deoxyribonucleotide)(n)-3'-hydroxyl
+ 5'-phospho-(deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m)
+ AMP + beta-nicotinamide D-nucleotide. {ECO:0000256|HAMAP-
Rule:MF_01588, ECO:0000256|SAAS:SAAS00702055}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000256|HAMAP-Rule:MF_01588};
Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
Evidence={ECO:0000256|HAMAP-Rule:MF_01588};
-!- SIMILARITY: Belongs to the NAD-dependent DNA ligase family. LigA
subfamily. {ECO:0000256|HAMAP-Rule:MF_01588,
ECO:0000256|SAAS:SAAS00572184}.
-!- CAUTION: Lacks conserved residue(s) required for the propagation
of feature annotation. {ECO:0000256|HAMAP-Rule:MF_01588}.
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EMBL; CP002130; AEI89398.1; -; Genomic_DNA.
RefSeq; WP_013951591.1; NC_015722.1.
STRING; 696127.midi_01121; -.
EnsemblBacteria; AEI89398; AEI89398; midi_01121.
KEGG; mmn:midi_01121; -.
eggNOG; ENOG4105C77; Bacteria.
eggNOG; COG0272; LUCA.
KO; K01972; -.
OMA; FTAKSPR; -.
OrthoDB; POG091H024G; -.
Proteomes; UP000006639; Chromosome.
GO; GO:0003911; F:DNA ligase (NAD+) activity; IEA:UniProtKB-HAMAP.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
CDD; cd00027; BRCT; 1.
Gene3D; 3.40.50.10190; -; 1.
HAMAP; MF_01588; DNA_ligase_A; 1.
InterPro; IPR001357; BRCT_dom.
InterPro; IPR033136; DNA_ligase_CS.
InterPro; IPR001679; DNAligase.
InterPro; IPR013839; DNAligase_adenylation.
InterPro; IPR013840; DNAligase_N.
InterPro; IPR012340; NA-bd_OB-fold.
InterPro; IPR004150; NAD_DNA_ligase_OB.
InterPro; IPR010994; RuvA_2-like.
InterPro; IPR004149; Znf_DNAligase_C4.
Pfam; PF00533; BRCT; 1.
Pfam; PF01653; DNA_ligase_aden; 1.
Pfam; PF03120; DNA_ligase_OB; 1.
Pfam; PF03119; DNA_ligase_ZBD; 1.
PIRSF; PIRSF001604; LigA; 1.
SMART; SM00292; BRCT; 1.
SMART; SM00532; LIGANc; 1.
SUPFAM; SSF47781; SSF47781; 1.
SUPFAM; SSF50249; SSF50249; 1.
SUPFAM; SSF52113; SSF52113; 1.
TIGRFAMs; TIGR00575; dnlj; 1.
PROSITE; PS50172; BRCT; 1.
PROSITE; PS01056; DNA_LIGASE_N2; 1.
3: Inferred from homology;
Complete proteome {ECO:0000313|Proteomes:UP000006639};
DNA damage {ECO:0000256|HAMAP-Rule:MF_01588,
ECO:0000256|SAAS:SAAS00572206};
DNA repair {ECO:0000256|HAMAP-Rule:MF_01588,
ECO:0000256|SAAS:SAAS00572206};
DNA replication {ECO:0000256|HAMAP-Rule:MF_01588,
ECO:0000256|SAAS:SAAS00572175};
Ligase {ECO:0000256|HAMAP-Rule:MF_01588,
ECO:0000256|SAAS:SAAS00572235, ECO:0000313|EMBL:AEI89398.1};
Magnesium {ECO:0000256|HAMAP-Rule:MF_01588,
ECO:0000256|SAAS:SAAS00769917};
Manganese {ECO:0000256|HAMAP-Rule:MF_01588};
Metal-binding {ECO:0000256|HAMAP-Rule:MF_01588,
ECO:0000256|SAAS:SAAS00572244};
NAD {ECO:0000256|HAMAP-Rule:MF_01588, ECO:0000256|SAAS:SAAS00572203};
Reference proteome {ECO:0000313|Proteomes:UP000006639};
Zinc {ECO:0000256|HAMAP-Rule:MF_01588, ECO:0000256|SAAS:SAAS00572196}.
DOMAIN 593 666 BRCT. {ECO:0000259|PROSITE:PS50172}.
NP_BIND 36 40 NAD. {ECO:0000256|HAMAP-Rule:MF_01588}.
NP_BIND 84 85 NAD. {ECO:0000256|HAMAP-Rule:MF_01588}.
ACT_SITE 115 115 N6-AMP-lysine intermediate.
{ECO:0000256|HAMAP-Rule:MF_01588}.
METAL 401 401 Zinc. {ECO:0000256|HAMAP-Rule:MF_01588}.
METAL 404 404 Zinc. {ECO:0000256|HAMAP-Rule:MF_01588}.
METAL 425 425 Zinc. {ECO:0000256|HAMAP-Rule:MF_01588}.
BINDING 113 113 NAD. {ECO:0000256|HAMAP-Rule:MF_01588}.
BINDING 136 136 NAD. {ECO:0000256|HAMAP-Rule:MF_01588}.
BINDING 170 170 NAD. {ECO:0000256|HAMAP-Rule:MF_01588}.
BINDING 283 283 NAD. {ECO:0000256|HAMAP-Rule:MF_01588}.
BINDING 307 307 NAD. {ECO:0000256|HAMAP-Rule:MF_01588}.
SEQUENCE 675 AA; 76778 MW; 67125CC0E051C786 CRC64;
MLSSLESDLK RIEFLRSELK RHNYLYYRLN KPKISDAEYD FLSKELERLE KLHGIEEVDS
PTQTVGGALD VKFKKVAHLR PMLSLGNAFS FSDIADFYER ITKVYPEVEF ICEPKIDGLS
FSALYQKGKL KYALTRGTGE YGEDITENFK QITAVPQTID YYEELEIRGE VYIRKDDFMA
LNNERSLKGE EEFANPRNAA AGSLRQLDSN ITKERKLRYF VWGGFFEHCV SQSNFLVKAK
ELGFCVNEDI ILCKTLEEVN SYYLKMSEKR AALPYDIDGL VYKVNNVKMQ QALGRTSKAP
RWAIAHKFPA EGAITQIEDI IVQVGRTGKL TPVALLKPVN VGGVLVSRAT LHNEDEIKRK
DFRIGDVVSI KRAGDVIPQV IEVDISKRNG NERIFEFPKN CPVCESSVEQ IEGEAAIRCT
GGRNCPAQLL EYLCYFVRKD AFDIIGLGEK QLEEFLEDGL IQEPADIFKI PEVGADILDN
LEKKTGWGKK SIANLLDAIE KSKRIRLDKF IYSLGIRHIG QVNAEIIAKH FRTFENFYGD
LKDNKFDALE RINGIGPTMI ESIESFFADV KNIKFIEELL QYITIEYMEE NDNIYSPLYN
KKIIFTGSLE SMARDRAEQI SKELGAKIVS SVSKKTDFVI AGSEAGSKLN KAKDLGVQVL
AEQEWLDMIN LLRTT


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