DNLJ_PARL1
ID DNLJ_PARL1 Reviewed; 710 AA.
AC A7HVV8;
DT 10-JUN-2008, integrated into UniProtKB/Swiss-Prot.
DT 11-SEP-2007, sequence version 1.
DT 03-AUG-2022, entry version 87.
DE RecName: Full=DNA ligase {ECO:0000255|HAMAP-Rule:MF_01588};
DE EC=6.5.1.2 {ECO:0000255|HAMAP-Rule:MF_01588};
DE AltName: Full=Polydeoxyribonucleotide synthase [NAD(+)] {ECO:0000255|HAMAP-Rule:MF_01588};
GN Name=ligA {ECO:0000255|HAMAP-Rule:MF_01588}; OrderedLocusNames=Plav_2432;
OS Parvibaculum lavamentivorans (strain DS-1 / DSM 13023 / NCIMB 13966).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Parvibaculaceae; Parvibaculum.
OX NCBI_TaxID=402881;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DS-1 / DSM 13023 / NCIMB 13966;
RX PubMed=22675581; DOI=10.4056/sigs.2215005;
RA Schleheck D., Weiss M., Pitluck S., Bruce D., Land M.L., Han S.,
RA Saunders E., Tapia R., Detter C., Brettin T., Han J., Woyke T., Goodwin L.,
RA Pennacchio L., Nolan M., Cook A.M., Kjelleberg S., Thomas T.;
RT "Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-
RT 1(T)).";
RL Stand. Genomic Sci. 5:298-310(2011).
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:0000255|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; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01588};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01588};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01588};
CC -!- SIMILARITY: Belongs to the NAD-dependent DNA ligase family. LigA
CC subfamily. {ECO:0000255|HAMAP-Rule:MF_01588}.
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DR EMBL; CP000774; ABS64041.1; -; Genomic_DNA.
DR RefSeq; WP_012111350.1; NC_009719.1.
DR AlphaFoldDB; A7HVV8; -.
DR SMR; A7HVV8; -.
DR STRING; 402881.Plav_2432; -.
DR EnsemblBacteria; ABS64041; ABS64041; Plav_2432.
DR KEGG; pla:Plav_2432; -.
DR eggNOG; COG0272; Bacteria.
DR HOGENOM; CLU_007764_2_1_5; -.
DR OMA; HDVEHEI; -.
DR OrthoDB; 241401at2; -.
DR Proteomes; UP000006377; 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; cd00114; LIGANc; 1.
DR Gene3D; 2.40.50.140; -; 1.
DR Gene3D; 3.40.50.10190; -; 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; IPR018239; DNA_ligase_AS.
DR InterPro; IPR033136; DNA_ligase_CS.
DR InterPro; IPR001679; DNAligase.
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 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; SSF47781; SSF47781; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR SUPFAM; SSF52113; SSF52113; 1.
DR TIGRFAMs; TIGR00575; dnlj; 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; DNA repair; DNA replication; Ligase; Magnesium; Manganese;
KW Metal-binding; NAD; Reference proteome; Zinc.
FT CHAIN 1..710
FT /note="DNA ligase"
FT /id="PRO_0000340362"
FT DOMAIN 633..710
FT /note="BRCT"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT ACT_SITE 138
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 53..57
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 102..103
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 136
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 159
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 196
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 312
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 336
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 429
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 432
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 453
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 459
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
SQ SEQUENCE 710 AA; 78597 MW; E48535719580091D CRC64;
MSAKRKSFDE ALAQKDVDHL TLEEAPEELE RLAAEIEKHD KLYYQKDAPR ISDAEYDTLR
RRNEAIEARY PELVREDSPS HRVGAQPADG FGKVVHKVPM LSLSNAFDDE DVRDFALRIR
RFLNLKEEDI LPITAEPKID GLSAALRYEK GKFVMGATRG DGREGENVTE NLKTIGDIPA
ELKGKNIPDV VEVRGEVYMS HEDFAALNER QREAGKPVFA NPRNAAAGSL RQLDAKITAS
RPLRFFAYTW GEMSDLPADT QSGVMDAFRK WGFTVNPLFG RCDTVEALID FYHDIEERRA
TLGYDIDGVV YKVDRLDWQN RLGFVSRSPR WALAHKFPAE QAMTVLEKIE IQVGRTGALT
PVARLTPVTV GGVVVSNATL HNADEIERLG VRPGDTVVVQ RAGDVIPQIV RVVEDRPRGK
KKFVFPDTCP ECGSHAVREV NPKTGKLDAV ARCTGGLVCP AQAVERLRHF VSRNAFDIEG
LGEKQIAAFF EDGLIKKPDD IFTLAARDAK SLKKLKDREG WGATSARKLF DAIDARREVE
LDRFIFGLGI RHVGETNARL LARSYGTLDH FEEQMRAAAD REDEAYAELL SIDGVGEVLA
ESIVDFFAEK HNREVLDGLR EAGVKGVPLP KQETSSPVAG KTVVFTGSLE KMTRSEAKAR
AEQLGAKVAG SVSAKTDILV AGADAGSKLA KARELGIEIL DEDQWIELAG
