ID D1BVV0_XYLCX Unreviewed; 830 AA.
AC D1BVV0;
DT 19-JAN-2010, integrated into UniProtKB/TrEMBL.
DT 19-JAN-2010, sequence version 1.
DT 27-MAR-2024, entry version 84.
DE RecName: Full=DNA ligase {ECO:0000256|HAMAP-Rule:MF_01588};
DE EC=6.5.1.2 {ECO:0000256|HAMAP-Rule:MF_01588};
DE AltName: Full=Polydeoxyribonucleotide synthase [NAD(+)] {ECO:0000256|HAMAP-Rule:MF_01588};
GN Name=ligA {ECO:0000256|HAMAP-Rule:MF_01588};
GN OrderedLocusNames=Xcel_2404 {ECO:0000313|EMBL:ACZ31419.1};
OS Xylanimonas cellulosilytica (strain DSM 15894 / CECT 5975 / LMG 20990 /
OS XIL07).
OC Bacteria; Actinomycetota; Actinomycetes; Micrococcales;
OC Promicromonosporaceae; Xylanimonas.
OX NCBI_TaxID=446471 {ECO:0000313|EMBL:ACZ31419.1, ECO:0000313|Proteomes:UP000002255};
RN [1] {ECO:0000313|Proteomes:UP000002255}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 15894 / CECT 5975 / LMG 20990 / XIL07
RC {ECO:0000313|Proteomes:UP000002255};
RG US DOE Joint Genome Institute (JGI-PGF);
RA Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H.,
RA Bruce D., Goodwin L., Pitluck S., Kyrpides N., Mavromatis K., Ivanova N.,
RA Mikhailova N., Foster B., Clum A., Brettin T., Detter J.C., Han C.,
RA Larimer F., Land M., Hauser L., Markowitz V., Cheng J.F., Hugenholtz P.,
RA Woyke T., Wu D., Gehrich-Schroeter G., Schneider S., Pukall S.R.,
RA Klenk H.P., Eisen J.A.;
RT "The complete chromosome of Xylanimonas cellulosilytica DSM 15894.";
RL Submitted (NOV-2009) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:ACZ31419.1, ECO:0000313|Proteomes:UP000002255}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 15894 / CECT 5975 / LMG 20990 / XIL07
RC {ECO:0000313|Proteomes:UP000002255};
RX PubMed=21304672; DOI=10.4056/sigs.571102;
RA Foster B., Pukall R., Abt B., Nolan M., Glavina Del Rio T., Chen F.,
RA Lucas S., Tice H., Pitluck S., Cheng J.-F., Chertkov O., Brettin T.,
RA Han C., Detter J.C., Bruce D., Goodwin L., Ivanova N., Mavromatis K.,
RA Pati A., Mikhailova N., Chen A., Palaniappan K., Land M., Hauser L.,
RA Chang Y.-J., Jeffries C.D., Chain P., Rohde M., Goeker M., Bristow J.,
RA Eisen J.A., Markowitz V., Hugenholtz P., Kyrpides N.C., Klenk H.-P.,
RA Lapidus A.;
RT "Complete genome sequence of Xylanimonas cellulosilytica type strain
RT (XIL07).";
RL Stand. Genomic Sci. 2:1-8(2010).
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};
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 ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; CP001821; ACZ31419.1; -; Genomic_DNA.
DR RefSeq; WP_012879161.1; NC_013530.1.
DR AlphaFoldDB; D1BVV0; -.
DR STRING; 446471.Xcel_2404; -.
DR KEGG; xce:Xcel_2404; -.
DR eggNOG; COG0272; Bacteria.
DR HOGENOM; CLU_007764_2_1_11; -.
DR OrthoDB; 9759736at2; -.
DR Proteomes; UP000002255; 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 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; 2.
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; 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 {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:UP000002255};
KW Zinc {ECO:0000256|ARBA:ARBA00022833, ECO:0000256|HAMAP-Rule:MF_01588}.
FT DOMAIN 732..801
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 44..48
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 93..94
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 341
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 365
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 461
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 464
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 480
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 486
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
SQ SEQUENCE 830 AA; 88647 MW; 5E7C79530D4C7832 CRC64;
MTTPDLSTAE LDEQAAQRRW AELRDLVEAD QRAYYEHDSP LVSDAEYDAR LHELAALEAA
HPALATPESP TQRVGGAAAS GFTTVEHVER MLSLDNVFSV DELRDWDARV ARDLGAGDVG
YLAEVKIDGL AIALLYEHGR LTRAATRGDG RTGEDVTVNA LRIADVPQQL DGEGHPALVE
VRGEIFIPTA SFTRLNELQE ELRARVVEDT RARQGARFDE EKARLAALRR FPTFANPRNA
AAGGLRQQLD KKDGLERDAG LARIESLRLY VHGIGALQWE AGEHAELGRQ SDAYSYFATW
GLPVSPHNRV VNGIDAVIEM IEHFGAHRHD IEHELDGIVV KVDALPDQQR LGATSRAPRW
AIAYKYPPEE VNTRLLAIQV GVGRTGRATP YAVMEPVLVA GSTVRQATLH NQDVVRAKGV
RVGDVVVLRK AGDVIPEILG PVPAAADDGF PRHDFVMPAQ CPECGTPLRP MKEGDVDLRC
PNARSCPAQV RGRVEHIGSR GGLDVEGLGE VAAAALTQPL EPADPPLDTE AGLFSLTIEE
LLPIRVVVRD PETGLPRPYD GVGESAELPT ADGATFTAKV VRPFQRLVER TYPPGTETMT
PAERRKAGIR KDHPVYGPAK SAQVLLDELD RAKTKDLWRQ LVSLNIRHVG PVAARALADW
FGSLDAIRAA SSEELAAVEG VGPVIGAELQ AWFDVDWHVD IVDSWTRAGV RFATPGHPGP
EAMAAQAAAG AAPQGPLAGL TVVVTGSLDG FTRDGAKEAI IAAGGKSAGS VSKKTDYVVV
GENAGSKAAK AEELGLPVLD EAGFVALLDG GPAALGADGG GDGDAADDQG
//
