ID A0A1V0GYX4_9RHOB Unreviewed; 845 AA.
AC A0A1V0GYX4;
DT 07-JUN-2017, integrated into UniProtKB/TrEMBL.
DT 07-JUN-2017, sequence version 1.
DT 24-JAN-2024, entry version 25.
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:ARC39037.1};
GN ORFNames=A6J80_22380 {ECO:0000313|EMBL:ARC39037.1};
OS Paracoccus yeei.
OG Plasmid unnamed5 {ECO:0000313|EMBL:ARC39037.1,
OG ECO:0000313|Proteomes:UP000191257}.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales;
OC Paracoccaceae; Paracoccus.
OX NCBI_TaxID=147645 {ECO:0000313|EMBL:ARC39037.1, ECO:0000313|Proteomes:UP000191257};
RN [1] {ECO:0000313|Proteomes:UP000191257}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=FDAARGOS_252 {ECO:0000313|Proteomes:UP000191257};
RC PLASMID=Plasmid unnamed5 {ECO:0000313|Proteomes:UP000191257};
RA Minogue T., Wolcott M., Wasieloski L., Aguilar W., Moore D., Tallon L.,
RA Sadzewicz L., Sengamalay N., Ott S., Godinez A., Nagaraj S., Nadendla S.,
RA Geyer C., Sichtig H.;
RT "FDA dAtabase for Regulatory Grade micrObial Sequences (FDA-ARGOS):
RT Supporting development and validation of Infectious Disease Dx tests.";
RL Submitted (MAR-2017) 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};
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DR EMBL; CP020445; ARC39037.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A1V0GYX4; -.
DR KEGG; pye:A6J80_22380; -.
DR eggNOG; COG1793; Bacteria.
DR eggNOG; COG3285; Bacteria.
DR Proteomes; UP000191257; Plasmid unnamed5.
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:0004527; F:exonuclease activity; 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; 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; BIFUNCTIONAL NON-HOMOLOGOUS END JOINING 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:ARC39037.1};
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 Plasmid {ECO:0000313|EMBL:ARC39037.1};
KW Reference proteome {ECO:0000313|Proteomes:UP000191257};
KW Transferase {ECO:0000256|ARBA:ARBA00022679}.
FT DOMAIN 333..424
FT /note="ATP-dependent DNA ligase family profile"
FT /evidence="ECO:0000259|PROSITE:PS50160"
FT REGION 1..30
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 162..236
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..17
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 162..176
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 185..220
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 845 AA; 92393 MW; C98779989109190C CRC64;
MALETYRKKR DFSATPEPEG RAGKTGGRSF VIQKHDATRL HYDFRLEMDG VLKSWAVTKG
PSLDPSEKRL AVHVEDHPLD YGDFEGTIPK GQYGGGTVIV WDRGTWSPIG DAEKAYAKGH
MEFELHGEKL SGRWHLVRMR GKSGEKRDNW LLIKGDDDQA RTEGDILEER PESVKTGRQI
AEVAEGVEKP ARKPATRKAD ARKPAPRKDA PRKDAPRKAA AKDAGTPAVK GAKRGALPDF
VPPMLATLVS SAPSGKEWLH EIKFDGYRLQ ARVEDGAVRL LTRSGLDWSE RFGDGVLKAL
AALPVKTALI DGELVVEAGS GASDFSALQA DLSEGRSDRF VFYAFDLMHL DGMDLRGAAL
AERKALLQPL LAEAPDTLRY SDHFAESGDM VLQHACQLSL EGIVSKLADS PYRAGRGKAW
VKSKCSARQE FVIGGYVPSM VSPKLIGSLV LGVHQGGTLR HVGRVGTGFS AAVAADLFRR
LEPMTRKTSP FDGKLTATEA RQVRYVEPEL VAEVEFRAWT ADGHLRHAAF RGLREDKPAA
EIVREEPKAG AKPAAPPRRT VRLTHPDRIY WPDAGVTKEG LADYYAEVWR HIAPHVVGRP
LALLRCPGGI DGQRFFQKHA WKGLNPRIVQ VRDPKDKAGE PLIAIEDLDG LMGLVQAAAL
EIHPWGSTLA SWEKPDQIVM DLDPGEGVPW TRVIEAALEI RQRLKDAGLA SFVKTSGGKG
LHVVAPLKPQ ATWPTVKSFT KALADSMAKD DPDRYVATVA KSKRQGKILI DYLRNQRGAT
AVAAYSTRAR PGAPVSTPLD WDELGPDIGP AHFTVANLPA RLAALTDNPW GGFRAAAVPL
PTRKR
//