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 03-AUG-2022, entry version 37.
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}.
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DR EMBL; AE000516; AAK45212.1; -; Genomic_DNA.
DR PIR; B70585; B70585.
DR RefSeq; WP_003898655.1; NZ_KK341227.1.
DR AlphaFoldDB; P9WNV2; -.
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 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 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; 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 DNA_BIND 137
FT /note="Interaction with target DNA"
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 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; for ligase activity"
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
