ID DNLJ_CLAM3 Reviewed; 853 AA.
AC A5CQU5;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 12-JUN-2007, sequence version 1.
DT 27-MAR-2024, entry version 100.
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=CMM_1404;
OS Clavibacter michiganensis subsp. michiganensis (strain NCPPB 382).
OC Bacteria; Actinomycetota; Actinomycetes; Micrococcales; Microbacteriaceae;
OC Clavibacter.
OX NCBI_TaxID=443906;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=NCPPB 382;
RX PubMed=18192381; DOI=10.1128/jb.01595-07;
RA Gartemann K.-H., Abt B., Bekel T., Burger A., Engemann J., Fluegel M.,
RA Gaigalat L., Goesmann A., Graefen I., Kalinowski J., Kaup O., Kirchner O.,
RA Krause L., Linke B., McHardy A., Meyer F., Pohle S., Rueckert C.,
RA Schneiker S., Zellermann E.-M., Puehler A., Eichenlaub R., Kaiser O.,
RA Bartels D.;
RT "The genome sequence of the tomato-pathogenic actinomycete Clavibacter
RT michiganensis subsp. michiganensis NCPPB382 reveals a large island involved
RT in pathogenicity.";
RL J. Bacteriol. 190:2138-2149(2008).
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; AM711867; CAN01449.1; -; Genomic_DNA.
DR RefSeq; WP_012038090.1; NC_009480.1.
DR AlphaFoldDB; A5CQU5; -.
DR SMR; A5CQU5; -.
DR KEGG; cmi:CMM_1404; -.
DR eggNOG; COG0272; Bacteria.
DR HOGENOM; CLU_007764_2_1_11; -.
DR OrthoDB; 9759736at2; -.
DR Proteomes; UP000001564; 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; 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 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.
PE 3: Inferred from homology;
KW DNA damage; DNA repair; DNA replication; Ligase; Magnesium; Manganese;
KW Metal-binding; NAD; Zinc.
FT CHAIN 1..853
FT /note="DNA ligase"
FT /id="PRO_0000313191"
FT DOMAIN 686..775
FT /note="BRCT"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT REGION 1..24
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 772..853
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 137
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 54..58
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 104..105
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 135
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 158
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 195
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 326
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 350
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 444
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 447
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 463
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 469
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
SQ SEQUENCE 853 AA; 90324 MW; 79DFDF381A057508 CRC64;
MSDTATDSPA ADDAVPATTP ADLEAASARV DALRTEIERH RDEYYGADAS TLSDAEYDAL
VHELEALEEA HPTLRSQDSP TQTVGGRAET TLFAPVTHAE RMLSLDNVFS EEELAEWAAK
VERDAGSGRV RYLSELKIDG LAINLRYEHG VLVTAATRGD GVVGEDVTQN VLTMGTVPER
LMGSGHPPLV EVRGEIFFPV AEFDELNARQ LEVGERVFAN PRNAAAGSLR QKEEGKSPAR
LELMRARIRR LRMLVHGIGA WPVRELASDA HVSAQSEVYG LLAGWGLPIS THFRVFDDIS
EVTEFVRRHG AHRAEVEHQI DGIVVKVDDL GLHEELGATS RAPRWATAYK YPPEEVNTTL
LDIVVSVGRT GRATPFAVME KVEVAGSEVR QATLHNQQVV KAKGVLIGDT VVLRKAGDVI
PEVLGPVVEL RDGTEREFVM PTLCPECQTP LRPAKEGDID LRCPNARSCP AQVRGRVEHV
ASRGALDIEG LGEVAAAALT QPLEPEDPPL ETEAGLFELT MADLVPITVV VRDAETGMVK
VDEKTGEAKR VTPFRRRRAP KRDGVFDPAA PWGDEDSVPS KSAEVLLENL DKAKTQDLWR
ILVALSIRHV GPVAARALAG WFGSLDAIRS ASREELAAVD GVGGIIADAL LDWFEVDWHR
EIVDRWRKAG VVMEVPGHPG PGAAAAAGGV LAGLTVVATG SLEGYTREGA LEAIMAAGGK
AGSSVSKKTH YVAAGPGAGS KLGKAEALGV RIIDAAEFRL LVEQGPDAIA LPDADPAADA
DPAAGADPAA DAAGAPAVGE AGEDASAEVK PKRARKRKAP AAADVASAAD VDADAAAVPE
PGEPGPGGAA ETP
//
