ID A0A372NRQ7_9SPHI Unreviewed; 635 AA.
AC A0A372NRQ7;
DT 07-NOV-2018, integrated into UniProtKB/TrEMBL.
DT 07-NOV-2018, sequence version 1.
DT 27-MAR-2024, entry version 24.
DE RecName: Full=DNA ligase (ATP) {ECO:0000256|ARBA:ARBA00012727};
DE EC=6.5.1.1 {ECO:0000256|ARBA:ARBA00012727};
GN Name=xth {ECO:0000313|EMBL:RFZ91320.1};
GN ORFNames=D0C36_20560 {ECO:0000313|EMBL:RFZ91320.1};
OS Mucilaginibacter conchicola.
OC Bacteria; Bacteroidota; Sphingobacteriia; Sphingobacteriales;
OC Sphingobacteriaceae; Mucilaginibacter.
OX NCBI_TaxID=2303333 {ECO:0000313|EMBL:RFZ91320.1, ECO:0000313|Proteomes:UP000264217};
RN [1] {ECO:0000313|EMBL:RFZ91320.1, ECO:0000313|Proteomes:UP000264217}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MYSH2 {ECO:0000313|EMBL:RFZ91320.1,
RC ECO:0000313|Proteomes:UP000264217};
RA Seo T.;
RT "Mucilaginibacter sp. MYSH2.";
RL Submitted (AUG-2018) to the EMBL/GenBank/DDBJ databases.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-
CC (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP +
CC diphosphate.; EC=6.5.1.1; Evidence={ECO:0000256|ARBA:ARBA00034003};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|PIRSR:PIRSR604808-2};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000256|PIRSR:PIRSR604808-2};
CC Note=Probably binds two magnesium or manganese ions per subunit.
CC {ECO:0000256|PIRSR:PIRSR604808-2};
CC -!- SIMILARITY: Belongs to the DNA repair enzymes AP/ExoA family.
CC {ECO:0000256|ARBA:ARBA00007092}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:RFZ91320.1}.
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; QWDC01000003; RFZ91320.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A372NRQ7; -.
DR OrthoDB; 9802472at2; -.
DR Proteomes; UP000264217; Unassembled WGS sequence.
DR GO; GO:0005524; F:ATP binding; IEA:InterPro.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0003910; F:DNA ligase (ATP) activity; IEA:UniProtKB-EC.
DR GO; GO:0008311; F:double-stranded DNA 3'-5' DNA exonuclease activity; IEA:UniProtKB-EC.
DR GO; GO:0004519; F:endonuclease activity; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006310; P:DNA recombination; IEA:InterPro.
DR GO; GO:0006281; P:DNA repair; IEA:InterPro.
DR CDD; cd07906; Adenylation_DNA_ligase_LigD_LigC; 1.
DR CDD; cd09086; ExoIII-like_AP-endo; 1.
DR CDD; cd07971; OBF_DNA_ligase_LigD; 1.
DR Gene3D; 3.30.1490.70; -; 1.
DR Gene3D; 3.30.470.30; DNA ligase/mRNA capping enzyme; 1.
DR Gene3D; 3.60.10.10; Endonuclease/exonuclease/phosphatase; 1.
DR Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 1.
DR InterPro; IPR004808; AP_endonuc_1.
DR InterPro; IPR020847; AP_endonuclease_F1_BS.
DR InterPro; IPR012309; DNA_ligase_ATP-dep_C.
DR InterPro; IPR012310; DNA_ligase_ATP-dep_cent.
DR InterPro; IPR016059; DNA_ligase_ATP-dep_CS.
DR InterPro; IPR036691; Endo/exonu/phosph_ase_sf.
DR InterPro; IPR005135; Endo/exonuclease/phosphatase.
DR InterPro; IPR037493; ExoIII-like.
DR InterPro; IPR014146; LigD_ligase_dom.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR NCBIfam; TIGR00195; exoDNase_III; 1.
DR NCBIfam; TIGR02779; NHEJ_ligase_lig; 1.
DR NCBIfam; TIGR00633; xth; 1.
DR PANTHER; PTHR43250; EXODEOXYRIBONUCLEASE III; 1.
DR PANTHER; PTHR43250:SF1; EXODEOXYRIBONUCLEASE III; 1.
DR Pfam; PF04679; DNA_ligase_A_C; 1.
DR Pfam; PF01068; DNA_ligase_A_M; 1.
DR Pfam; PF03372; Exo_endo_phos; 1.
DR SUPFAM; SSF56091; DNA ligase/mRNA capping enzyme, catalytic domain; 1.
DR SUPFAM; SSF56219; DNase I-like; 1.
DR SUPFAM; SSF50249; Nucleic acid-binding proteins; 1.
DR PROSITE; PS00726; AP_NUCLEASE_F1_1; 1.
DR PROSITE; PS51435; AP_NUCLEASE_F1_4; 1.
DR PROSITE; PS00333; DNA_LIGASE_A2; 1.
DR PROSITE; PS50160; DNA_LIGASE_A3; 1.
PE 3: Inferred from homology;
KW Hydrolase {ECO:0000313|EMBL:RFZ91320.1};
KW Ligase {ECO:0000256|ARBA:ARBA00022598};
KW Magnesium {ECO:0000256|PIRSR:PIRSR604808-2};
KW Manganese {ECO:0000256|PIRSR:PIRSR604808-2};
KW Metal-binding {ECO:0000256|PIRSR:PIRSR604808-2}.
FT DOMAIN 386..526
FT /note="ATP-dependent DNA ligase family profile"
FT /evidence="ECO:0000259|PROSITE:PS50160"
FT ACT_SITE 106
FT /evidence="ECO:0000256|PIRSR:PIRSR604808-1"
FT ACT_SITE 147
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000256|PIRSR:PIRSR604808-1"
FT ACT_SITE 248
FT /note="Proton acceptor"
FT /evidence="ECO:0000256|PIRSR:PIRSR604808-1"
FT BINDING 7
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|PIRSR:PIRSR604808-2"
FT BINDING 34
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|PIRSR:PIRSR604808-2"
FT BINDING 147
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|PIRSR:PIRSR604808-2"
FT BINDING 149
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|PIRSR:PIRSR604808-2"
FT BINDING 247
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|PIRSR:PIRSR604808-2"
FT BINDING 248
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|PIRSR:PIRSR604808-2"
FT SITE 149
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000256|PIRSR:PIRSR604808-3"
FT SITE 218
FT /note="Important for catalytic activity"
FT /evidence="ECO:0000256|PIRSR:PIRSR604808-3"
FT SITE 248
FT /note="Interaction with DNA substrate"
FT /evidence="ECO:0000256|PIRSR:PIRSR604808-3"
SQ SEQUENCE 635 AA; 72545 MW; C24E770CD2E6470A CRC64;
MKIATYNING INGRLEILLR WIKEAKPDIV CLQELKAENR AFPEQQLKTA GYNAIWQGQK
SWNGVAILAK SEIRELRRDL PGEDEKFTHS RYIEAFVDGI VIGCIYLPNG NPWPGGKFDY
KLRWFQRLAD HAKDLVNRDL PVMLIGDYNV MPTELDTYKP EKYEANALFR PESRKAYQDL
IAQGWTDAIR TLFPNERIYT FWDYLRDAYG RNAGLRLDHF LLNPVIVNRL KTGQVDKHVR
GWQGSSDHAP VWIELSEHDL PRKKPKTTTS MIVVNKAQVS ELQNLLAKAP TSAPPLKLQP
MKATLVREPF NDAGWLYEIK WDGYRALAVV NQQEAELISR NNISFDQFHP IAEALKKWNA
NAIIDGEIVV LGADGKSDFS AIQNWQRRKD GRLVYNVFDI LWYEGRDLRQ LPLTERKAIL
DVVLPTDDTI RQSKAFAVNG IDFFHAAEKA GIEGIMAKKA DSTYTSGDRS RQWLKVKVER
RQEVVIGAFT RNSGTDKLFS ALAIGVYQKG VLRYIGKVGT GWSGKKQKEM MAEFEPLITD
VCPFEVEPDV DETSQYRPRR LGAKPFWLKP ELVCEVNIAD ITGDGKVRQA SFKGMRRDKD
PKEVILEVPA DRQSTVAEAD ESAERIKKKL LKRKP
//
