LIGD_MYCBO
ID LIGD_MYCBO Reviewed; 759 AA.
AC P59971; A0A1R3XWV9; X2BG90;
DT 31-OCT-2003, integrated into UniProtKB/Swiss-Prot.
DT 31-OCT-2003, sequence version 1.
DT 03-AUG-2022, entry version 99.
DE RecName: Full=Multifunctional non-homologous end joining protein LigD;
DE AltName: Full=NHEJ DNA polymerase;
DE Includes:
DE RecName: Full=DNA repair polymerase;
DE Short=Pol;
DE AltName: Full=Polymerase/primase;
DE Includes:
DE RecName: Full=3'-phosphoesterase;
DE Short=3'-ribonuclease/3'-phosphatase;
DE Short=PE;
DE Includes:
DE RecName: Full=DNA ligase;
DE Short=Lig;
DE EC=6.5.1.1;
DE AltName: Full=Polydeoxyribonucleotide synthase [ATP];
GN Name=ligD; OrderedLocusNames=BQ2027_MB0963;
OS Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=233413;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-935 / AF2122/97;
RX PubMed=12788972; DOI=10.1073/pnas.1130426100;
RA Garnier T., Eiglmeier K., Camus J.-C., Medina N., Mansoor H., Pryor M.,
RA Duthoy S., Grondin S., Lacroix C., Monsempe C., Simon S., Harris B.,
RA Atkin R., Doggett J., Mayes R., Keating L., Wheeler P.R., Parkhill J.,
RA Barrell B.G., Cole S.T., Gordon S.V., Hewinson R.G.;
RT "The complete genome sequence of Mycobacterium bovis.";
RL Proc. Natl. Acad. Sci. U.S.A. 100:7877-7882(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], AND GENOME REANNOTATION.
RC STRAIN=ATCC BAA-935 / AF2122/97;
RX PubMed=28385856; DOI=10.1128/genomea.00157-17;
RA Malone K.M., Farrell D., Stuber T.P., Schubert O.T., Aebersold R.,
RA Robbe-Austerman S., Gordon S.V.;
RT "Updated reference genome sequence and annotation of Mycobacterium bovis
RT AF2122/97.";
RL Genome Announc. 5:E00157-E00157(2017).
CC -!- FUNCTION: With Ku forms a non-homologous end joining (NHEJ) DNA repair
CC enzyme which repairs DNA double strand breaks (DSB) with reduced
CC fidelity. Ligates dsDNA, repairs incompatible DSB which require 3'-
CC resection, gap filling and ligation. Has several activities; DNA-
CC directed DNA or RNA polymerase on 5'-overhangs, terminal transferase
CC (extending ssDNA or blunt dsDNA in a non-templated fashion,
CC preferentially with rNTPs), DNA-dependent RNA primase (synthesizes
CC short RNAs on unprimed closed ssDNA) and 3'-phosphoesterase on ssDNA.
CC {ECO:0000250}.
CC -!- FUNCTION: The preference of the polymerase domain for rNTPs over dNTPs
CC may be advantageous in dormant cells, where the dNTP pool may be
CC limiting. {ECO:0000250}.
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;
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC Note=Binds 4 Mn(2+); 2 Mn(2+) for polymerase/primase activity, 1 each
CC for 3-phosphoesterase and ligase. {ECO:0000250};
CC -!- SUBUNIT: Interacts with Ku. {ECO:0000250}.
CC -!- MISCELLANEOUS: LigD has variable architecture; domain order can be
CC permutated, domains can be independently encoded, while some bacteria
CC lack the 3'-phosphoesterase domain entirely.
CC -!- SIMILARITY: In the N-terminal section; belongs to the LigD polymerase
CC family. {ECO:0000305}.
CC -!- SIMILARITY: In the central section; belongs to the LigD 3'-
CC phosphoesterase family. {ECO:0000305}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the ATP-dependent DNA
CC ligase family. {ECO:0000305}.
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DR EMBL; LT708304; SIT99561.1; -; Genomic_DNA.
DR RefSeq; NP_854620.1; NC_002945.3.
DR RefSeq; WP_003898655.1; NC_002945.4.
DR AlphaFoldDB; P59971; -.
DR SMR; P59971; -.
DR EnsemblBacteria; SIT99561; SIT99561; BQ2027_MB0963.
DR PATRIC; fig|233413.5.peg.1048; -.
DR OMA; QWLAHRM; -.
DR Proteomes; UP000001419; Chromosome.
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; cd04863; MtLigD_Pol_like; 1.
DR Gene3D; 2.40.50.140; -; 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; IPR033649; MtLigD_Pol-like.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR Pfam; PF04679; DNA_ligase_A_C; 1.
DR Pfam; PF01068; DNA_ligase_A_M; 1.
DR Pfam; PF13298; LigD_N; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR TIGRFAMs; TIGR02777; LigD_PE_dom; 1.
DR TIGRFAMs; TIGR02778; ligD_pol; 1.
DR TIGRFAMs; TIGR02779; NHEJ_ligase_lig; 1.
DR PROSITE; PS50160; DNA_LIGASE_A3; 1.
PE 3: Inferred from homology;
KW ATP-binding; DNA damage; DNA recombination; DNA repair; DNA-binding;
KW DNA-directed DNA polymerase; Exonuclease; Hydrolase; Ligase; Manganese;
KW Metal-binding; Multifunctional enzyme; Nuclease; Nucleotide-binding;
KW Nucleotidyltransferase; Transferase.
FT CHAIN 1..759
FT /note="Multifunctional non-homologous end joining protein
FT LigD"
FT /id="PRO_0000059626"
FT DNA_BIND 13..16
FT /evidence="ECO:0000250"
FT DNA_BIND 26
FT /evidence="ECO:0000250"
FT DNA_BIND 53..55
FT /evidence="ECO:0000250"
FT DNA_BIND 63..67
FT /evidence="ECO:0000250"
FT DNA_BIND 71
FT /evidence="ECO:0000250"
FT DNA_BIND 83..88
FT /evidence="ECO:0000250"
FT DNA_BIND 104
FT /evidence="ECO:0000250"
FT DNA_BIND 234..235
FT /evidence="ECO:0000250"
FT REGION 9..261
FT /note="DNA repair polymerase domain (Pol)"
FT REGION 297..446
FT /note="3'-phosphoesterase domain (PE)"
FT REGION 460..757
FT /note="Ligase domain (Lig)"
FT REGION 740..759
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 743..759
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 481
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000250"
FT BINDING 52
FT /ligand="substrate"
FT /ligand_note="for polymerase activity"
FT /evidence="ECO:0000250"
FT BINDING 111
FT /ligand="substrate"
FT /ligand_note="for polymerase activity"
FT /evidence="ECO:0000250"
FT BINDING 137..139
FT /ligand="substrate"
FT /ligand_note="for polymerase activity"
FT /evidence="ECO:0000250"
FT BINDING 137
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 137
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 139
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 139
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 172..178
FT /ligand="substrate"
FT /ligand_note="for polymerase activity"
FT /evidence="ECO:0000250"
FT BINDING 227
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 230
FT /ligand="substrate"
FT /ligand_note="for polymerase activity"
FT /evidence="ECO:0000250"
FT BINDING 236
FT /ligand="substrate"
FT /ligand_note="for polymerase activity"
FT /evidence="ECO:0000250"
FT BINDING 244
FT /ligand="substrate"
FT /ligand_note="for polymerase activity"
FT /evidence="ECO:0000250"
FT BINDING 331
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="3"
FT /ligand_note="catalytic; for 3'-phosphoesterase activity"
FT /evidence="ECO:0000250"
FT BINDING 337
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="3"
FT /ligand_note="catalytic; for 3'-phosphoesterase activity"
FT /evidence="ECO:0000250"
FT BINDING 339
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="3"
FT /ligand_note="catalytic; for 3'-phosphoesterase activity"
FT /evidence="ECO:0000250"
FT BINDING 483
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="4"
FT /evidence="ECO:0000250"
FT BINDING 613
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="4"
FT /evidence="ECO:0000250"
FT SITE 373
FT /note="Transition state stabilizer; for 3'-phosphoesterase
FT activity"
FT /evidence="ECO:0000250"
SQ SEQUENCE 759 AA; 83625 MW; 8E1B59E06A356B3D CRC64;
MGSASEQRVT LTNADKVLYP ATGTTKSDIF DYYAGVAEVM LGHIAGRPAT RKRWPNGVDQ
PAFFEKQLAL SAPPWLSRAT VAHRSGTTTY PIIDSATGLA WIAQQAALEV HVPQWRFVAE
PGSGELNPGP ATRLVFDLDP GEGVMMAQLA EVARAVRDLL ADIGLVTFPV TSGSKGLHLY
TPLDEPVSSR GATVLAKRVA QRLEQAMPAL VTSTMTKSLR AGKVFVDWSQ NSGSKTTIAP
YSLRGRTHPT VAAPRTWAEL DDPALRQLSY DEVLTRIARD GDLLERLDAD APVADRLTRY
RRMRDASKTP EPIPTAKPVT GDGNTFVIQE HHARRPHYDF RLERDGVLVS WAVPKNLPDN
TSVNHLAIHT EDHPLEYATF EGAIPSGEYG AGKVIIWDSG TYDTEKFHDD PHTGEVIVNL
HGGRISGRYA LIRTNGDRWL AHRLKNQKDQ KVFEFDNLAP MLATHGTVAG LKASQWAFEG
KWDGYRLLVE ADHGAVRLRS RSGRDVTAEY PQLRALAEDL ADHHVVLDGE AVVLDSSGVP
SFSQMQNRGR DTRVEFWAFD LLYLDGRALL GTRYQDRRKL LETLANATSL TVPELLPGDG
AQAFACSRKH GWEGVIAKRR DSRYQPGRRC ASWVKDKHWN TQEVVIGGWR AGEGGRSSGV
GSLLMGIPGP GGLQFAGRVG TGLSERELAN LKEMLAPLHT DESPFDVPLP ARDAKGITYV
KPALVAEVRY SEWTPEGRLR QSSWRGLRPD KKPSEVVRE
