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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   13-FEB-2019, entry version 27.
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.,
RA   Hickey E.K., Kolonay J.F., Nelson W.C., Umayam L.A., Ermolaeva M.D.,
RA   Salzberg S.L., Delcher A., Utterback T.R., Weidman J.F., Khouri H.M.,
RA   Gill J., Mikula A., Bishai W., Jacobs W.R. Jr., Venter J.C.,
RA   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
CC       repairs on incompatible DSB which require 3'-resection, gap
CC       filling and ligation. Anneals the 3' overhanging strands from
CC       opposing breaks to form a gapped intermediate, which then can be
CC       extended in trans by using the termini as primers for extension of
CC       the annealed break. Binds to the recessed 5'-phosphate moiety of
CC       the downstream DNA strand forming a stable synaptic complex even
CC       when the 3'-protruding ends of the template DNA strands are not
CC       complementary. {ECO:0000250}.
CC   -!- FUNCTION: The preference of the polymerase domain for rNTPs over
CC       dNTPs may be advantageous in dormant cells, where the dNTP pool is
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
CC       each 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
CC       polymerase 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-
CC       dependent DNA ligase family. {ECO:0000305}.
DR   EMBL; AE000516; AAK45212.1; -; Genomic_DNA.
DR   PIR; B70585; B70585.
DR   RefSeq; WP_003898655.1; NZ_KK341227.1.
DR   ProteinModelPortal; P9WNV2; -.
DR   SMR; P9WNV2; -.
DR   EnsemblBacteria; AAK45212; AAK45212; MT0965.
DR   KEGG; mtc:MT0965; -.
DR   PATRIC; fig|83331.31.peg.1035; -.
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; Complete proteome; DNA damage; DNA recombination;
KW   DNA repair; DNA-binding; DNA-directed DNA polymerase; Exonuclease;
KW   Host-virus interaction; Hydrolase; Ligase; Manganese; Metal-binding;
KW   Multifunctional enzyme; Nuclease; Nucleotide-binding;
KW   Nucleotidyltransferase; Transferase.
FT   CHAIN         1    759       Multifunctional non-homologous end
FT                                joining DNA repair protein LigD.
FT                                /FTId=PRO_0000427062.
FT   DNA_BIND     13     16       Interaction with target DNA.
FT                                {ECO:0000250}.
FT   DNA_BIND     26     26       Interaction with target DNA.
FT                                {ECO:0000250}.
FT   DNA_BIND     53     55       Interaction with target DNA.
FT                                {ECO:0000250}.
FT   DNA_BIND     63     67       Interaction with target DNA.
FT                                {ECO:0000250}.
FT   DNA_BIND     71     71       Interaction with target DNA.
FT                                {ECO:0000250}.
FT   DNA_BIND     83     88       Interaction with target DNA.
FT                                {ECO:0000250}.
FT   DNA_BIND    104    104       Interaction with target DNA.
FT                                {ECO:0000250}.
FT   NP_BIND     137    139       Substrate; for polymerase activity.
FT                                {ECO:0000250}.
FT   DNA_BIND    137    137       Interaction with target DNA.
FT                                {ECO:0000250}.
FT   NP_BIND     172    178       Substrate; for polymerase activity.
FT                                {ECO:0000250}.
FT   DNA_BIND    215    220       Interaction with target DNA.
FT                                {ECO:0000250}.
FT   DNA_BIND    227    235       Interaction with target DNA.
FT                                {ECO:0000250}.
FT   REGION        1    411       Not required for ligase activity.
FT                                {ECO:0000250}.
FT   REGION        9    261       DNA repair polymerase domain (Pol);
FT                                interacts with Ku. {ECO:0000250}.
FT   REGION      297    446       3-phosphoesterase domain (PE).
FT                                {ECO:0000250}.
FT   REGION      460    757       Ligase domain (Lig). {ECO:0000250}.
FT   ACT_SITE    481    481       N6-AMP-lysine intermediate; for ligase
FT                                activity. {ECO:0000250}.
FT   METAL       137    137       Manganese 1. {ECO:0000250}.
FT   METAL       137    137       Manganese 2. {ECO:0000250}.
FT   METAL       139    139       Manganese 1. {ECO:0000250}.
FT   METAL       139    139       Manganese 2. {ECO:0000250}.
FT   METAL       227    227       Manganese 2. {ECO:0000250}.
FT   METAL       331    331       Manganese 3; via pros nitrogen;
FT                                catalytic; for 3'-phosphoesterase
FT                                activity. {ECO:0000250}.
FT   METAL       337    337       Manganese 3; via tele nitrogen;
FT                                catalytic; for 3'-phosphoesterase
FT                                activity. {ECO:0000250}.
FT   METAL       339    339       Manganese 3; catalytic; for 3'-
FT                                phosphoesterase activity. {ECO:0000250}.
FT   METAL       483    483       Manganese 4. {ECO:0000250}.
FT   METAL       613    613       Manganese 4. {ECO:0000250}.
FT   BINDING      52     52       Substrate; for polymerase activity.
FT                                {ECO:0000250}.
FT   BINDING     111    111       Substrate; for polymerase activity.
FT                                {ECO:0000250}.
FT   BINDING     230    230       Substrate; for polymerase activity.
FT                                {ECO:0000250}.
FT   BINDING     236    236       Substrate; for polymerase activity.
FT                                {ECO:0000250}.
FT   BINDING     244    244       Substrate; for polymerase activity.
FT                                {ECO:0000250}.
FT   SITE        373    373       Transition state stabilizer; for 3'-
FT                                phosphoesterase activity. {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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