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Database: UniProt/SWISS-PROT
Entry: LIGD_MYCTO
LinkDB: LIGD_MYCTO
Original site: LIGD_MYCTO 
ID   LIGD_MYCTO              Reviewed;         759 AA.
AC   P9WNV2; L0T5C5; O05865; P71571;
DT   16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT   16-APR-2014, sequence version 1.
DT   26-FEB-2020, entry version 31.
DE   RecName: Full=Multifunctional non-homologous end joining DNA repair protein LigD;
DE            Short=NHEJ DNA repair protein D;
DE   AltName: Full=Mt-Lig;
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=MT0965;
OS   Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh).
OC   Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC   Mycobacterium; Mycobacterium tuberculosis complex.
OX   NCBI_TaxID=83331;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=CDC 1551 / Oshkosh;
RX   PubMed=12218036; DOI=10.1128/jb.184.19.5479-5490.2002;
RA   Fleischmann R.D., Alland D., Eisen J.A., Carpenter L., White O.,
RA   Peterson J.D., DeBoy R.T., Dodson R.J., Gwinn M.L., Haft D.H., Hickey E.K.,
RA   Kolonay J.F., Nelson W.C., Umayam L.A., Ermolaeva M.D., Salzberg S.L.,
RA   Delcher A., Utterback T.R., Weidman J.F., Khouri H.M., Gill J., Mikula A.,
RA   Bishai W., Jacobs W.R. Jr., Venter J.C., Fraser C.M.;
RT   "Whole-genome comparison of Mycobacterium tuberculosis clinical and
RT   laboratory strains.";
RL   J. Bacteriol. 184:5479-5490(2002).
CC   -!- FUNCTION: With Ku forms a non-homologous end joining (NHEJ) repair
CC       enzyme which repairs DNA double-strand breaks (DSB) with reduced
CC       fidelity. Recognizes, processes and reseals DSBs, including repairs on
CC       incompatible DSB which require 3'-resection, gap filling and ligation.
CC       Anneals the 3' overhanging strands from opposing breaks to form a
CC       gapped intermediate, which then can be extended in trans by using the
CC       termini as primers for extension of the annealed break. Binds to the
CC       recessed 5'-phosphate moiety of the downstream DNA strand forming a
CC       stable synaptic complex even when the 3'-protruding ends of the
CC       template DNA strands are not complementary. {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 is limiting.
CC       {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: Monomer. Component of the NHEJ repair enzyme with mKu (By
CC       similarity). {ECO:0000250}.
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}.
DR   EMBL; AE000516; AAK45212.1; -; Genomic_DNA.
DR   PIR; B70585; B70585.
DR   RefSeq; WP_003898655.1; NZ_KK341227.1.
DR   SMR; P9WNV2; -.
DR   EnsemblBacteria; AAK45212; AAK45212; MT0965.
DR   KEGG; mtc:MT0965; -.
DR   PATRIC; fig|83331.31.peg.1035; -.
DR   HOGENOM; CLU_008325_2_1_11; -.
DR   KO; K01971; -.
DR   BioCyc; MTBCDC1551:GT3Z-5311-MONOMER; -.
DR   Proteomes; UP000001020; 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   GO; GO:0016032; P:viral process; IEA:UniProtKB-KW.
DR   CDD; cd04863; MtLigD_Pol_like; 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; Host-virus interaction;
KW   Hydrolase; Ligase; Manganese; Metal-binding; Multifunctional enzyme;
KW   Nuclease; Nucleotide-binding; Nucleotidyltransferase; Transferase.
FT   CHAIN           1..759
FT                   /note="Multifunctional non-homologous end joining DNA
FT                   repair protein LigD"
FT                   /id="PRO_0000427062"
FT   DNA_BIND        13..16
FT                   /note="Interaction with target DNA"
FT                   /evidence="ECO:0000250"
FT   DNA_BIND        26
FT                   /note="Interaction with target DNA"
FT                   /evidence="ECO:0000250"
FT   DNA_BIND        53..55
FT                   /note="Interaction with target DNA"
FT                   /evidence="ECO:0000250"
FT   DNA_BIND        63..67
FT                   /note="Interaction with target DNA"
FT                   /evidence="ECO:0000250"
FT   DNA_BIND        71
FT                   /note="Interaction with target DNA"
FT                   /evidence="ECO:0000250"
FT   DNA_BIND        83..88
FT                   /note="Interaction with target DNA"
FT                   /evidence="ECO:0000250"
FT   DNA_BIND        104
FT                   /note="Interaction with target DNA"
FT                   /evidence="ECO:0000250"
FT   NP_BIND         137..139
FT                   /note="Substrate; for polymerase activity"
FT                   /evidence="ECO:0000250"
FT   DNA_BIND        137
FT                   /note="Interaction with target DNA"
FT                   /evidence="ECO:0000250"
FT   NP_BIND         172..178
FT                   /note="Substrate; for polymerase activity"
FT                   /evidence="ECO:0000250"
FT   DNA_BIND        215..220
FT                   /note="Interaction with target DNA"
FT                   /evidence="ECO:0000250"
FT   DNA_BIND        227..235
FT                   /note="Interaction with target DNA"
FT                   /evidence="ECO:0000250"
FT   REGION          1..411
FT                   /note="Not required for ligase activity"
FT                   /evidence="ECO:0000250"
FT   REGION          9..261
FT                   /note="DNA repair polymerase domain (Pol); interacts with
FT                   Ku"
FT                   /evidence="ECO:0000250"
FT   REGION          297..446
FT                   /note="3-phosphoesterase domain (PE)"
FT                   /evidence="ECO:0000250"
FT   REGION          460..757
FT                   /note="Ligase domain (Lig)"
FT                   /evidence="ECO:0000250"
FT   ACT_SITE        481
FT                   /note="N6-AMP-lysine intermediate; for ligase activity"
FT                   /evidence="ECO:0000250"
FT   METAL           137
FT                   /note="Manganese 1"
FT                   /evidence="ECO:0000250"
FT   METAL           137
FT                   /note="Manganese 2"
FT                   /evidence="ECO:0000250"
FT   METAL           139
FT                   /note="Manganese 1"
FT                   /evidence="ECO:0000250"
FT   METAL           139
FT                   /note="Manganese 2"
FT                   /evidence="ECO:0000250"
FT   METAL           227
FT                   /note="Manganese 2"
FT                   /evidence="ECO:0000250"
FT   METAL           331
FT                   /note="Manganese 3; via pros nitrogen; catalytic; for 3'-
FT                   phosphoesterase activity"
FT                   /evidence="ECO:0000250"
FT   METAL           337
FT                   /note="Manganese 3; via tele nitrogen; catalytic; for 3'-
FT                   phosphoesterase activity"
FT                   /evidence="ECO:0000250"
FT   METAL           339
FT                   /note="Manganese 3; catalytic; for 3'-phosphoesterase
FT                   activity"
FT                   /evidence="ECO:0000250"
FT   METAL           483
FT                   /note="Manganese 4"
FT                   /evidence="ECO:0000250"
FT   METAL           613
FT                   /note="Manganese 4"
FT                   /evidence="ECO:0000250"
FT   BINDING         52
FT                   /note="Substrate; for polymerase activity"
FT                   /evidence="ECO:0000250"
FT   BINDING         111
FT                   /note="Substrate; for polymerase activity"
FT                   /evidence="ECO:0000250"
FT   BINDING         230
FT                   /note="Substrate; for polymerase activity"
FT                   /evidence="ECO:0000250"
FT   BINDING         236
FT                   /note="Substrate; for polymerase activity"
FT                   /evidence="ECO:0000250"
FT   BINDING         244
FT                   /note="Substrate; for polymerase activity"
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
//
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