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Multifunctional non-homologous end joining protein LigD (NHEJ DNA polymerase) [Includes: DNA repair polymerase (Pol) (Polymerase/primase); 3'-phosphoesterase (3'-ribonuclease/3'-phosphatase) (PE); DNA ligase (Lig) (EC 6.5.1.1) (Polydeoxyribonucleotide synthase [ATP])]

 LIGD_MYCS2              Reviewed;         762 AA.
A0R3R7; I7FKR9;
19-MAR-2014, integrated into UniProtKB/Swiss-Prot.
19-MAR-2014, sequence version 2.
07-JUN-2017, entry version 84.
RecName: Full=Multifunctional non-homologous end joining protein LigD;
AltName: Full=NHEJ DNA polymerase;
Includes:
RecName: Full=DNA repair polymerase;
Short=Pol;
AltName: Full=Polymerase/primase;
Includes:
RecName: Full=3'-phosphoesterase;
Short=3'-ribonuclease/3'-phosphatase;
Short=PE;
Includes:
RecName: Full=DNA ligase;
Short=Lig;
EC=6.5.1.1;
AltName: Full=Polydeoxyribonucleotide synthase [ATP];
Name=ligD; OrderedLocusNames=MSMEG_5570, MSMEI_5419;
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155).
Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
Mycobacterium.
NCBI_TaxID=246196;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 700084 / mc(2)155;
Fleischmann R.D., Dodson R.J., Haft D.H., Merkel J.S., Nelson W.C.,
Fraser C.M.;
Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases.
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 700084 / mc(2)155;
PubMed=17295914; DOI=10.1186/gb-2007-8-2-r20;
Deshayes C., Perrodou E., Gallien S., Euphrasie D., Schaeffer C.,
Van-Dorsselaer A., Poch O., Lecompte O., Reyrat J.-M.;
"Interrupted coding sequences in Mycobacterium smegmatis: authentic
mutations or sequencing errors?";
Genome Biol. 8:R20.1-R20.9(2007).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 700084 / mc(2)155;
PubMed=18955433; DOI=10.1101/gr.081901.108;
Gallien S., Perrodou E., Carapito C., Deshayes C., Reyrat J.-M.,
Van Dorsselaer A., Poch O., Schaeffer C., Lecompte O.;
"Ortho-proteogenomics: multiple proteomes investigation through
orthology and a new MS-based protocol.";
Genome Res. 19:128-135(2009).
[4]
FUNCTION, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF ASP-136 AND
ASP-138.
STRAIN=ATCC 700084 / mc(2)155;
PubMed=15778718; DOI=10.1038/nsmb915;
Gong C., Bongiorno P., Martins A., Stephanou N.C., Zhu H., Shuman S.,
Glickman M.S.;
"Mechanism of nonhomologous end-joining in mycobacteria: a low-
fidelity repair system driven by Ku, ligase D and ligase C.";
Nat. Struct. Mol. Biol. 12:304-312(2005).
[5]
FUNCTION, PROBABLE ACTIVE SITE, AND MUTAGENESIS OF LYS-484.
STRAIN=ATCC 700084 / mc(2)155;
PubMed=16476729; DOI=10.1074/jbc.M513550200;
Akey D., Martins A., Aniukwu J., Glickman M.S., Shuman S.,
Berger J.M.;
"Crystal structure and nonhomologous end-joining function of the
ligase component of Mycobacterium DNA ligase D.";
J. Biol. Chem. 281:13412-13423(2006).
[6]
FUNCTION IN VIRAL REPLICATION, INTERACTION WITH VIRAL KU HOMOLOGS,
DISRUPTION PHENOTYPE, AND MUTAGENESIS OF 136-ASP--ASP-138 AND LYS-484.
STRAIN=ATCC 700084 / mc(2)155;
PubMed=16949369; DOI=10.1016/j.molcel.2006.07.009;
Pitcher R.S., Tonkin L.M., Daley J.M., Palmbos P.L., Green A.J.,
Velting T.L., Brzostek A., Korycka-Machala M., Cresawn S., Dziadek J.,
Hatfull G.F., Wilson T.E., Doherty A.J.;
"Mycobacteriophage exploit NHEJ to facilitate genome
circularization.";
Mol. Cell 23:743-748(2006).
[7]
FUNCTION, AND MUTAGENESIS OF 136-ASP--ASP-138.
PubMed=16446439; DOI=10.1073/pnas.0509083103;
Zhu H., Nandakumar J., Aniukwu J., Wang L.K., Glickman M.S.,
Lima C.D., Shuman S.;
"Atomic structure and nonhomologous end-joining function of the
polymerase component of bacterial DNA ligase D.";
Proc. Natl. Acad. Sci. U.S.A. 103:1711-1716(2006).
[8]
FUNCTION, AND DISRUPTION PHENOTYPE.
STRAIN=ATCC 700084 / mc(2)155;
PubMed=17360246; DOI=10.1016/j.dnarep.2007.02.009;
Pitcher R.S., Green A.J., Brzostek A., Korycka-Machala M., Dziadek J.,
Doherty A.J.;
"NHEJ protects mycobacteria in stationary phase against the harmful
effects of desiccation.";
DNA Repair 6:1271-1276(2007).
[9]
DISRUPTION PHENOTYPE.
STRAIN=ATCC 700084 / mc(2)155;
PubMed=17496093; DOI=10.1128/JB.00332-07;
Stephanou N.C., Gao F., Bongiorno P., Ehrt S., Schnappinger D.,
Shuman S., Glickman M.S.;
"Mycobacterial nonhomologous end joining mediates mutagenic repair of
chromosomal double-strand DNA breaks.";
J. Bacteriol. 189:5237-5246(2007).
[10]
FUNCTION IN GAP FILLING, COFACTOR, DOMAIN, AND DNA-BINDING.
PubMed=17174332; DOI=10.1016/j.jmb.2006.10.046;
Pitcher R.S., Brissett N.C., Picher A.J., Andrade P., Juarez R.,
Thompson D., Fox G.C., Blanco L., Doherty A.J.;
"Structure and function of a mycobacterial NHEJ DNA repair
polymerase.";
J. Mol. Biol. 366:391-405(2007).
[11]
FUNCTION, DOMAIN, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF
136-ASP--ASP-138; GLU-310; HIS-336; LYS-484 AND GLU-533.
STRAIN=ATCC 700084 / mc(2)155;
PubMed=18281464; DOI=10.1101/gad.1631908;
Aniukwu J., Glickman M.S., Shuman S.;
"The pathways and outcomes of mycobacterial NHEJ depend on the
structure of the broken DNA ends.";
Genes Dev. 22:512-527(2008).
[12]
DISRUPTION PHENOTYPE.
STRAIN=ATCC 700084 / mc(2)155;
PubMed=21219454; DOI=10.1111/j.1365-2958.2010.07463.x;
Gupta R., Barkan D., Redelman-Sidi G., Shuman S., Glickman M.S.;
"Mycobacteria exploit three genetically distinct DNA double-strand
break repair pathways.";
Mol. Microbiol. 79:316-330(2011).
[13]
INTERACTION WITH SIR2, AND SUBUNIT.
STRAIN=ATCC 700084 / mc(2)155;
PubMed=21637345; DOI=10.1371/journal.pone.0020045;
Li Z., Wen J., Lin Y., Wang S., Xue P., Zhang Z., Zhou Y., Wang X.,
Sui L., Bi L.J., Zhang X.E.;
"A Sir2-like protein participates in mycobacterial NHEJ.";
PLoS ONE 6:E20045-E20045(2011).
-!- FUNCTION: With Ku forms a non-homologous end joining (NHEJ) repair
enzyme which repairs blunt-end and 5'-overhang DNA double strand
breaks (DSB) with about 50% fidelity, and DSB with non-
complementary 3' ends. Plays a partial role in NHEJ during 3'-
overhang repair. NHEJ repairs DSB with blunt ends and 5' overhangs
with a high level of nucleotide insertion/deletion, without a need
for microhomology. Acts as a DNA ligase on singly nicked dsDNA, as
a DNA-directed DNA polymerase on 5' overhangs, and adds non-
templated nucleotides to 3' overhangs (terminal transferase).
Fills in gaps in dsDNA, prefers a 5'-phosphate in the gap. Site-
directed mutations leading to ligase loss alter the bias from
insertion to deletion mutations, and indicate another ligase
(LigC1 and/or LigC2) can compensate.
-!- FUNCTION: The preference of the polymerase domain for rNTPs over
dNTPs may be advantageous in dormant cells, where the dNTP pool
may be limiting. {ECO:0000250, ECO:0000269|PubMed:15778718,
ECO:0000269|PubMed:16446439, ECO:0000269|PubMed:16476729,
ECO:0000269|PubMed:16949369, ECO:0000269|PubMed:17174332,
ECO:0000269|PubMed:17360246, ECO:0000269|PubMed:18281464}.
-!- FUNCTION: The ligase activity is required for replication of
viruses with short cos ends (4 bases) such as Mycobacterium phage
Omega and Corndog, but not D29 which has a 9 base cos end.
Stimulates dsDNA end joining by LigD; when expressed with
endogenous or Mycobacterium phage Omega Ku, can reconstitute NHEJ
in Saccharomyces cerevisiae.
-!- CATALYTIC ACTIVITY: ATP + (deoxyribonucleotide)(n)-3'-hydroxyl +
5'-phospho-(deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) +
AMP + diphosphate.
-!- COFACTOR:
Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
Note=Binds 4 Mn(2+); 2 Mn(2+) for polymerase/primase activity, 1
each for 3-phosphoesterase and ligase. {ECO:0000250};
-!- SUBUNIT: Interacts with Sir2 and probably also with Ku; may form a
trimeric complex during NHEJ. Interacts with Mycobacterium phage
Omega and Corndog Ku homologs (AC Q853W0, AC Q856K7).
{ECO:0000269|PubMed:16949369, ECO:0000269|PubMed:21637345}.
-!- DOMAIN: The N-terminal divalent cation-dependent
polymerase/primase domain (Pol) functions as an independent domain
(PubMed:17174332). Deletion of the Pol domain (residues 1-288)
yields a protein severely impaired in NHEJ on blunt or 5'-
overhangs (PubMed:18281464). {ECO:0000269|PubMed:17174332,
ECO:0000269|PubMed:18281464}.
-!- DOMAIN: The central 3'-phosphoesterase domain (PE)
(PubMed:17174332). Mutations in the PE domain argue against this
domain being involved in residue deletion during NHEJ
(PubMed:18281464). {ECO:0000269|PubMed:17174332,
ECO:0000269|PubMed:18281464}.
-!- DOMAIN: The C-terminal ATP-dependent ligase domain (Lig) functions
as an independent domain (PubMed:17174332). Loss of the Lig domain
(residues 449 to 762) forces NHEJ to rely on another ligase, which
decreases fidelity for blunt and 5'-overhang DSB
(PubMed:18281464). {ECO:0000269|PubMed:17174332,
ECO:0000269|PubMed:18281464}.
-!- DISRUPTION PHENOTYPE: Not essential for growth in the absence of
DNA damage. 320-fold reduction in NHEJ on blunt-ended DSB, with a
loss of nucleotide insertions. 100-fold less efficient repair of
5'-overhang DSBs with little nucleotide insertion. Upon deletion,
the fidelity of DNA repair depends on the form of the DSB; for
blunt-ends fidelity is very low, for 5'-overhangs remains 50%
faithful, for 3'-overhangs repair is fully faithful. NHEJ on
blunt-ended plasmid is 24-fold further decreased in a triple
ligC1-ligC2-ligD deletion. In quadruple ligB-ligC1-ligC2-ligD
deletions NHEJ on blunt and 5'-overhangs is 0.22 and 0.12% of
wild-type respectively; only 4-fold decrease in 3'-overhang NHEJ.
100-fold decrease in viability when exposed to ionizing radiation
in late and stationary phase; 1000-fold decrease in a double ligD-
ku deletion. Decreased resistance to desiccation-induced DSBs.
Mycobacterium phage Omega and Corndog are unable to infect a
deletion strain. Loss of NHEJ on incompatible 3'-chromosomal
overhangs, partial reduction in single-strand annealing DSB
repair. {ECO:0000269|PubMed:15778718, ECO:0000269|PubMed:16949369,
ECO:0000269|PubMed:17360246, ECO:0000269|PubMed:17496093,
ECO:0000269|PubMed:18281464, ECO:0000269|PubMed:21219454}.
-!- MISCELLANEOUS: LigD has variable architecture; domain order can be
permutated, domains can be independently encoded, while some
bacteria lack the 3'-phosphoesterase domain entirely.
-!- SIMILARITY: In the N-terminal section; belongs to the LigD
polymerase family. {ECO:0000305}.
-!- SIMILARITY: In the central section; belongs to the LigD 3'-
phosphoesterase family. {ECO:0000305}.
-!- SIMILARITY: In the C-terminal section; belongs to the ATP-
dependent DNA ligase family. {ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=ABK75957.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; CP000480; ABK75957.1; ALT_INIT; Genomic_DNA.
EMBL; CP001663; AFP41860.1; -; Genomic_DNA.
RefSeq; YP_889805.1; NC_008596.1.
SMR; A0R3R7; -.
STRING; 246196.MSMEG_5570; -.
EnsemblBacteria; ABK75957; ABK75957; MSMEG_5570.
EnsemblBacteria; AFP41860; AFP41860; MSMEI_5419.
GeneID; 4535131; -.
KEGG; msg:MSMEI_5419; -.
KEGG; msm:MSMEG_5570; -.
PATRIC; fig|246196.19.peg.5431; -.
eggNOG; ENOG4105DQE; Bacteria.
eggNOG; COG1793; LUCA.
eggNOG; COG3285; LUCA.
HOGENOM; HOG000222509; -.
KO; K10747; -.
OrthoDB; POG091H0AZ9; -.
Proteomes; UP000000757; Chromosome.
Proteomes; UP000006158; Chromosome.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
GO; GO:0003910; F:DNA ligase (ATP) activity; IEA:UniProtKB-EC.
GO; GO:0003887; F:DNA-directed DNA polymerase activity; IEA:UniProtKB-KW.
GO; GO:0004527; F:exonuclease activity; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
GO; GO:0006303; P:double-strand break repair via nonhomologous end joining; IMP:UniProtKB.
GO; GO:0016032; P:viral process; IEA:UniProtKB-KW.
CDD; cd04863; MtLigD_Pol_like; 1.
InterPro; IPR012309; DNA_ligase_ATP-dep_C.
InterPro; IPR012310; DNA_ligase_ATP-dep_cent.
InterPro; IPR014146; LigD_ligase_dom.
InterPro; IPR014144; LigD_PE_domain.
InterPro; IPR014145; LigD_pol_dom.
InterPro; IPR033649; MtLigD_Pol-like.
InterPro; IPR012340; NA-bd_OB-fold.
Pfam; PF04679; DNA_ligase_A_C; 1.
Pfam; PF01068; DNA_ligase_A_M; 1.
Pfam; PF13298; LigD_N; 1.
SUPFAM; SSF50249; SSF50249; 1.
TIGRFAMs; TIGR02777; LigD_PE_dom; 1.
TIGRFAMs; TIGR02778; ligD_pol; 1.
TIGRFAMs; TIGR02779; NHEJ_ligase_lig; 1.
PROSITE; PS50160; DNA_LIGASE_A3; 1.
1: Evidence at protein level;
ATP-binding; Complete proteome; DNA damage; DNA recombination;
DNA repair; DNA-binding; DNA-directed DNA polymerase; Exonuclease;
Host-virus interaction; Hydrolase; Ligase; Manganese; Metal-binding;
Multifunctional enzyme; Nuclease; Nucleotide-binding;
Nucleotidyltransferase; Reference proteome; Transferase.
CHAIN 1 762 Multifunctional non-homologous end
joining protein LigD.
/FTId=PRO_0000425949.
DNA_BIND 18 21 {ECO:0000250}.
DNA_BIND 31 31 {ECO:0000250}.
DNA_BIND 58 60 {ECO:0000250}.
DNA_BIND 68 72 {ECO:0000250}.
DNA_BIND 76 76 {ECO:0000250}.
DNA_BIND 88 93 {ECO:0000250}.
DNA_BIND 109 109 {ECO:0000250}.
NP_BIND 136 138 Substrate; for polymerase activity.
{ECO:0000250}.
NP_BIND 171 177 Substrate; for polymerase activity.
{ECO:0000250}.
DNA_BIND 233 234 {ECO:0000250}.
REGION 14 260 DNA repair polymerase domain (Pol).
REGION 296 453 3'-phosphoesterase domain (PE).
REGION 463 760 Ligase domain (Lig).
ACT_SITE 484 484 N6-AMP-lysine intermediate.
{ECO:0000305}.
METAL 136 136 Manganese 1. {ECO:0000250}.
METAL 136 136 Manganese 2. {ECO:0000250}.
METAL 138 138 Manganese 1. {ECO:0000250}.
METAL 138 138 Manganese 2. {ECO:0000250}.
METAL 226 226 Manganese 2. {ECO:0000250}.
METAL 330 330 Manganese 3; via pros nitrogen;
catalytic; for 3'-phosphoesterase
activity. {ECO:0000250}.
METAL 336 336 Manganese 3; via tele nitrogen;
catalytic; for 3'-phosphoesterase
activity. {ECO:0000250}.
METAL 338 338 Manganese 3; catalytic; for 3'-
phosphoesterase activity. {ECO:0000250}.
METAL 486 486 Manganese 4. {ECO:0000250}.
METAL 616 616 Manganese 4. {ECO:0000250}.
BINDING 57 57 Substrate; for polymerase activity.
{ECO:0000250}.
BINDING 116 116 Substrate; for polymerase activity.
{ECO:0000250}.
BINDING 229 229 Substrate; for polymerase activity.
{ECO:0000250}.
BINDING 235 235 Substrate; for polymerase activity.
{ECO:0000250}.
BINDING 243 243 Substrate; for polymerase activity.
{ECO:0000250}.
SITE 372 372 Transition state stabilizer; for 3'-
phosphoesterase activity. {ECO:0000250}.
MUTAGEN 136 138 DLD->ALA: In vivo 30% reduction in NHEJ
on blunt-end DSB, fidelity doubles, loss
of non-templated nucleotide insertion
during NHEJ. No effect on efficiency of
DSB on 5'- or 3'-overhangs, increased
fidelity on 5'-overhangs. No effect on
viral infection.
{ECO:0000269|PubMed:16446439,
ECO:0000269|PubMed:16949369,
ECO:0000269|PubMed:18281464}.
MUTAGEN 136 136 D->A: Loss of templated and non-templated
DNA synthesis, but not ligase activity.
{ECO:0000269|PubMed:15778718}.
MUTAGEN 138 138 D->A: Loss of templated and non-templated
DNA synthesis, but not ligase activity.
{ECO:0000269|PubMed:15778718}.
MUTAGEN 310 310 E->A: No effect on efficiency or fidelity
on NHEJ of blunt, 5'-overhangs or 3'-
overhangs. {ECO:0000269|PubMed:18281464}.
MUTAGEN 336 336 H->A: No effect on efficiency or fidelity
on NHEJ of blunt, 5'-overhangs or 3'-
overhangs. {ECO:0000269|PubMed:18281464}.
MUTAGEN 484 484 K->A: 2.7 and 3.7-fold decrease in
efficiency of NHEJ on blunt and 5'-
overhangs respectively. Considerably
decreases NHEJ fidelity on both DSBs. No
viral infection.
{ECO:0000269|PubMed:16476729,
ECO:0000269|PubMed:16949369,
ECO:0000269|PubMed:18281464}.
MUTAGEN 533 533 E->A: 3-fold and 9-fold decrease in
efficiency of NHEJ on blunt and 5'-
overhangs respectively, with very
decreased fidelity on both DSBs. No viral
infection. {ECO:0000269|PubMed:18281464}.
SEQUENCE 762 AA; 85516 MW; ED1853A73A3E552E CRC64;
MARHPWGMER YERVRLTNPD KVLYPATGTT KAEVFDYYLS IAQVMVPHIA GRPVTRKRWP
NGVAEEAFFE KQLASSAPSW LERGSITHKS GTTTYPIINT REGLAWVAQQ ASLEVHVPQW
RFEDGDQGPA TRIVFDLDPG EGVTMTQLCE IAHEVRALMT DLDLETYPLT SGSKGLHLYV
PLAEPISSRG ASVLARRVAQ QLEQAMPKLV TATMTKSLRA GKVFLDWSQN NAAKTTIAPY
SLRGRDHPTV AAPRTWDEIA DPELRHLRFD EVLDRLDEYG DLLAPLDADA PIADKLTTYR
SMRDASKTPE PVPKEIPKTG NNDKFVIQEH HARRLHYDLR LERDGVLVSF AVPKNLPETT
AENRLAVHTE DHPIEYLAFH GSIPKGEYGA GDMVIWDSGS YETEKFRVPE ELDNPDDSHG
EIIVTLHGEK VDGRYALIQT KGKNWLAHRM KDQKNARPED FAPMLATEGS VAKYKAKQWA
FEGKWDGYRV IIDADHGQLQ IRSRTGREVT GEYPQFKALA ADLAEHHVVL DGEAVALDES
GVPSFGQMQN RARSTRVEFW AFDILWLDGR SLLRAKYSDR RKILEALADG GGLIVPDQLP
GDGPEAMEHV RKKRFEGVVA KKWDSTYQPG RRSSSWIKDK IWNTQEVVIG GWRQGEGGRS
SGIGALVLGI PGPEGLQFVG RVGTGFTEKE LSKLKDMLKP LHTDESPFNA PLPKVDARGV
TFVRPELVGE VRYSERTSDG RLRQPSWRGL RPDKTPDEVV WE


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