ID A0A1I0SQ34_9SPHI Unreviewed; 960 AA.
AC A0A1I0SQ34;
DT 22-NOV-2017, integrated into UniProtKB/TrEMBL.
DT 22-NOV-2017, sequence version 1.
DT 24-JAN-2024, entry version 33.
DE RecName: Full=DNA ligase (ATP) {ECO:0000256|ARBA:ARBA00012727};
DE EC=6.5.1.1 {ECO:0000256|ARBA:ARBA00012727};
DE AltName: Full=NHEJ DNA polymerase {ECO:0000256|ARBA:ARBA00029943};
GN ORFNames=SAMN04488511_102339 {ECO:0000313|EMBL:SFA41527.1};
OS Pedobacter suwonensis.
OC Bacteria; Bacteroidota; Sphingobacteriia; Sphingobacteriales;
OC Sphingobacteriaceae; Pedobacter.
OX NCBI_TaxID=332999 {ECO:0000313|EMBL:SFA41527.1, ECO:0000313|Proteomes:UP000198836};
RN [1] {ECO:0000313|Proteomes:UP000198836}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 18130 {ECO:0000313|Proteomes:UP000198836};
RA Varghese N., Submissions S.;
RL Submitted (OCT-2016) 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 -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000256|ARBA:ARBA00001936};
CC -!- SIMILARITY: Belongs to the DNA repair enzymes AP/ExoA family.
CC {ECO:0000256|ARBA:ARBA00007092}.
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DR EMBL; FOJM01000002; SFA41527.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A1I0SQ34; -.
DR STRING; 332999.SAMN04488511_102339; -.
DR OrthoDB; 9802472at2; -.
DR Proteomes; UP000198836; Unassembled WGS sequence.
DR GO; GO:0005524; F:ATP binding; IEA:InterPro.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003910; F:DNA ligase (ATP) activity; IEA:UniProtKB-EC.
DR GO; GO:0003887; F:DNA-directed DNA polymerase activity; IEA:UniProtKB-KW.
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; cd04865; LigD_Pol_like_2; 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; 3.90.920.10; DNA primase, PRIM domain; 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; 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; IPR014145; LigD_pol_dom.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR014143; NHEJ_ligase_prk.
DR NCBIfam; TIGR00195; exoDNase_III; 1.
DR NCBIfam; TIGR02778; ligD_pol; 1.
DR NCBIfam; TIGR02779; NHEJ_ligase_lig; 1.
DR NCBIfam; TIGR02776; NHEJ_ligase_prk; 1.
DR NCBIfam; TIGR00633; xth; 1.
DR PANTHER; PTHR43250; -; 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 Pfam; PF21686; LigD_Prim-Pol; 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; PS50160; DNA_LIGASE_A3; 1.
PE 3: Inferred from homology;
KW DNA-binding {ECO:0000256|ARBA:ARBA00023125};
KW DNA-directed DNA polymerase {ECO:0000256|ARBA:ARBA00022932};
KW Exonuclease {ECO:0000256|ARBA:ARBA00022839};
KW Hydrolase {ECO:0000256|ARBA:ARBA00022801};
KW Ligase {ECO:0000256|ARBA:ARBA00022598};
KW Magnesium {ECO:0000256|PIRSR:PIRSR604808-2};
KW Manganese {ECO:0000256|ARBA:ARBA00023211, ECO:0000256|PIRSR:PIRSR604808-2};
KW Metal-binding {ECO:0000256|PIRSR:PIRSR604808-2};
KW Multifunctional enzyme {ECO:0000256|ARBA:ARBA00023268};
KW Nuclease {ECO:0000256|ARBA:ARBA00022722};
KW Nucleotidyltransferase {ECO:0000256|ARBA:ARBA00022695};
KW Transferase {ECO:0000256|ARBA:ARBA00022679}.
FT DOMAIN 386..513
FT /note="ATP-dependent DNA ligase family profile"
FT /evidence="ECO:0000259|PROSITE:PS50160"
FT REGION 625..653
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
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 960 AA; 109078 MW; 96D8D55137806659 CRC64;
MKIASYNING INGRLENLLR WLKEAAPDVV CLQELKCEDK NFPVSKINQA GYHAVWRGEK
SWNGVAILSK NEIKELRRDL PGGDDEFTHS RYLEAFTSGV VIGCIYLPNG NPYPGPKFEY
KKRWFSRLQE HAKALLATGL PVILAGDYNV MPTELDTYKP EKYRENALFQ KEIRDDFAML
VDQGWTDAIR MLYPGKRIYT FWDYLRKAYD RDAGLRLDHF LLTADLAEKL TDAKVDKAVR
GWKGSSDHAP VWIELSEKPA RNKTSRSKRI GGKKIPVLTR EIQNLLKQAD ETEMPIGIKP
MKATLVDEPF DQPGWLYEVK WDGYRAIAYV EKSGAKLFSR NNLEFGQFTT ITAALEALKL
DAVFDGEIVA LKEDGSADFG ALQNWKNTQR AELIYYVFDI LWFKGYSLLS ITLNDRRKIL
EAVMPREHPE IRVSKAYHTS GLDFFEAAKK MKLEGIIAKR ADSFYSSDSR SREWLKIKAK
RRQEVVIGGY TRNEGTEKYF SALTLGVYGP KGNLHYIGKV GTGFNQQSQK ELMAVFENLT
TTICPFETEP DVDEPSQFRP RRMGAKPTWL KPDLVCEIEF AELTSDGKLR QASFKGLRED
KSPNEVVFEY EKDTASITQE VSLQHQLAEQ PHKPSAGSTR NRKGKKLKDK GLLLTGSSDT
QDKIVDGHPL KFTHLSKLYW PEEQVSKRDM FNYYDQVAPL MLPYLLDRPM SLNRFPGGIH
SASFYQKNVK ETAPSWARTM PHTNEKGEEK SYLLGKDRAT LLWMASLGCI EMNPWFSRAS
SPDYPDYCVI DLDPDKNTFE QVIQAAQVTR SILDSMGVPS FPKTSGSTGI HIYIPLGAKY
TYEQSQLFAN LIVRQVNREL PKFTTLEPTI SRRGGKMYLD FLQNRPGATI AGVYSLRPKP
GATVSMPLLW DEVKPGLKMR DFTIFNAVDR LSETGDLFSG VLGKGIDMAE VLSTAQHLFS
//