ID A0A2U0SAC0_9SPHN Unreviewed; 850 AA.
AC A0A2U0SAC0;
DT 18-JUL-2018, integrated into UniProtKB/TrEMBL.
DT 18-JUL-2018, sequence version 1.
DT 27-MAR-2024, entry version 27.
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 Name=ligD {ECO:0000313|EMBL:PVX28337.1};
GN ORFNames=DD559_02440 {ECO:0000313|EMBL:PVX28337.1};
OS Sphingomonas pokkalii.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales;
OC Sphingomonadaceae; Sphingomonas.
OX NCBI_TaxID=2175090 {ECO:0000313|EMBL:PVX28337.1, ECO:0000313|Proteomes:UP000245890};
RN [1] {ECO:0000313|EMBL:PVX28337.1, ECO:0000313|Proteomes:UP000245890}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=L3B27 {ECO:0000313|EMBL:PVX28337.1,
RC ECO:0000313|Proteomes:UP000245890};
RA Menon R., Kumari S., Rameshkumar N.;
RT "Description of Sphingomonas pokkalii sp nov, isolated from the rhizosphere
RT of saline tolerant pokkali rice and its draft genome analysis.";
RL Submitted (MAY-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=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000256|ARBA:ARBA00001936};
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:PVX28337.1}.
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DR EMBL; QENQ01000001; PVX28337.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A2U0SAC0; -.
DR OrthoDB; 9802472at2; -.
DR Proteomes; UP000245890; Unassembled WGS sequence.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
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:0004527; F:exonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
DR GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
DR CDD; cd07906; Adenylation_DNA_ligase_LigD_LigC; 1.
DR CDD; cd07971; OBF_DNA_ligase_LigD; 1.
DR CDD; cd04862; PaeLigD_Pol_like; 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; 2.40.50.140; Nucleic acid-binding proteins; 1.
DR InterPro; IPR012309; DNA_ligase_ATP-dep_C.
DR InterPro; IPR012310; DNA_ligase_ATP-dep_cent.
DR InterPro; IPR014146; LigD_ligase_dom.
DR InterPro; IPR014144; LigD_PE_domain.
DR InterPro; IPR014145; LigD_pol_dom.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR014143; NHEJ_ligase_prk.
DR InterPro; IPR033651; PaeLigD_Pol-like.
DR NCBIfam; TIGR02777; LigD_PE_dom; 1.
DR NCBIfam; TIGR02778; ligD_pol; 1.
DR NCBIfam; TIGR02779; NHEJ_ligase_lig; 1.
DR NCBIfam; TIGR02776; NHEJ_ligase_prk; 1.
DR PANTHER; PTHR42705; BIFUNCTIONAL NON-HOMOLOGOUS END JOINING PROTEIN LIGD; 1.
DR PANTHER; PTHR42705:SF2; MULTIFUNCTIONAL NON-HOMOLOGOUS END JOINING DNA REPAIR PROTEIN LIGD; 1.
DR Pfam; PF04679; DNA_ligase_A_C; 1.
DR Pfam; PF01068; DNA_ligase_A_M; 1.
DR Pfam; PF13298; LigD_N; 1.
DR Pfam; PF21686; LigD_Prim-Pol; 1.
DR SUPFAM; SSF56091; DNA ligase/mRNA capping enzyme, catalytic domain; 1.
DR SUPFAM; SSF50249; Nucleic acid-binding proteins; 1.
DR PROSITE; PS50160; DNA_LIGASE_A3; 1.
PE 4: Predicted;
KW ATP-binding {ECO:0000256|ARBA:ARBA00022840};
KW DNA damage {ECO:0000256|ARBA:ARBA00022763};
KW DNA recombination {ECO:0000256|ARBA:ARBA00023172};
KW DNA repair {ECO:0000256|ARBA:ARBA00023204};
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, ECO:0000313|EMBL:PVX28337.1};
KW Manganese {ECO:0000256|ARBA:ARBA00023211};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723};
KW Multifunctional enzyme {ECO:0000256|ARBA:ARBA00023268};
KW Nuclease {ECO:0000256|ARBA:ARBA00022722};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741};
KW Nucleotidyltransferase {ECO:0000256|ARBA:ARBA00022695};
KW Transferase {ECO:0000256|ARBA:ARBA00022679}.
FT DOMAIN 354..481
FT /note="ATP-dependent DNA ligase family profile"
FT /evidence="ECO:0000259|PROSITE:PS50160"
FT REGION 188..260
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 189..215
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 232..248
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 850 AA; 93354 MW; EC15657ACE6A55C7 CRC64;
MPEPGSLARY HAKRDFAKTS EPAGTVAKGS GNRFLVQKHD ATRLHWDFRL EVDGVLKSWA
VTRGPSLDPD EKRLAVRTED HPLSYADFEG TIPKGEYGGG TVMLWDSGTW EPIPGKRAED
LDKGHLHFVL HGHRMQGEWL LIRLKPRGKE KAENWLLRKI DDGFAGATDE LVETGLTSVT
TGRTMQEIAE GAKPEHVEGR NRPALHRHPR EGGDPLAKRS AAGAETPPSM DSRLRGSDKG
EIGARSRKKP KAPPFQQPQR ATLVDTVPTG NQWLHEIKYD GYRALIATGT GGPRLYTRSG
LDWTERFPGI AEAAATLPPG ALLDGEIVAM KDGKPDFSTL QEAISAGGGG LICFAFDLLA
EAGEDLTALP QLERKERLRS LLDGADDRIR FSEHVLGQGE KLFAAMCRDR FEGVVSKRAD
APYRGTRSKV WLKIKCTHRQ EFVILGWIPS TARGREFKSL LLGLNGRDGL VYAGKVGTGF
DRETLRSLRE RLDQRATDMP AAKVPRPEAR GAHWVQPELV AEVAFAEFTA EKVVRHASFL
GLREDKAADA VVAEEPAALP ETAASTIKIS SRDRVIFPES KLTKGDLADY YAAVAPIALP
WLADRPISLV RCPQGRARQC FFQKHDAGSF GEQVHHVDIR EKDGSTEPYL YLSDADGMLA
CVQMGTIEFH GWGSRVGDVE KPDRLVFDLD PDEGLDFAAV KKAAAYLKEQ LAEIGLTSWP
MLSGGKGVHV VVPLVPRAEW PAAKSFCERF AKALAQAEPD RFTANLKKIS RTGRIFIDYL
RNQRGATAVL PYVARARANA PVAAPVTWSE LRTIDSAGTF TIRDADALIA RAASRALRGW
GTADQTLPDL
//
