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Database: UniProt
Entry: A0A1I0SQ34_9SPHI
LinkDB: A0A1I0SQ34_9SPHI
Original site: A0A1I0SQ34_9SPHI 
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
//
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