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A0R3R7 (LIGD_MYCS2) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 57. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Multifunctional non-homologous end joining protein LigD
Alternative name(s):
NHEJ DNA polymerase

Including the following 3 domains:

  1. DNA repair polymerase
    Short name=Pol
    Alternative name(s):
    Polymerase/primase
  2. 3'-phosphoesterase
    Short name=3'-ribonuclease/3'-phosphatase
    Short name=PE
  3. DNA ligase
    Short name=Lig
    EC=6.5.1.1
    Alternative name(s):
    Polydeoxyribonucleotide synthase [ATP]
Gene names
Name:ligD
Ordered Locus Names:MSMEG_5570, MSMEI_5419
OrganismMycobacterium smegmatis (strain ATCC 700084 / mc(2)155) [Reference proteome] [HAMAP]
Taxonomic identifier246196 [NCBI]
Taxonomic lineageBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeMycobacteriaceaeMycobacterium

Protein attributes

Sequence length762 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

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. Ref.4 Ref.5 Ref.6 Ref.7 Ref.8 Ref.10 Ref.11

The preference of the polymerase domain for rNTPs over dNTPs may be advantageous in dormant cells, where the dNTP pool may be limiting By similarity. Ref.4 Ref.5 Ref.6 Ref.7 Ref.8 Ref.10 Ref.11

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. Ref.4 Ref.5 Ref.6 Ref.7 Ref.8 Ref.10 Ref.11

Catalytic activity

ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).

Cofactor

Binds 4 Mn2+; 2 Mn2+ for polymerase/primase activity, 1 each for 3-phosphoesterase and ligase By similarity. Ref.10

Subunit structure

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). Ref.6 Ref.13

Domain

The N-terminal divalent cation-dependent polymerase/primase domain (Pol) functions as an independent domain (Ref.10). Deletion of the Pol domain (residues 1-288) yields a protein severely impaired in NHEJ on blunt or 5'-overhangs (Ref.11). Ref.10 Ref.11

The central 3'-phosphoesterase domain (PE) (Ref.10). Mutations in the PE domain argue against this domain being involved in residue deletion during NHEJ (Ref.11). Ref.10 Ref.11

The C-terminal ATP-dependent ligase domain (Lig) functions as an independent domain (Ref.10). 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 (Ref.11). Ref.10 Ref.11

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. Ref.4 Ref.6 Ref.8 Ref.9 Ref.11 Ref.12

Miscellaneous

LigD has variable architecture; domain order can be permutated, domains can be independently encoded, while some bacteria lack the 3'-phosphoesterase domain entirely.

Sequence similarities

In the N-terminal section; belongs to the LigD polymerase family.

In the central section; belongs to the LigD 3'-phosphoesterase family.

In the C-terminal section; belongs to the ATP-dependent DNA ligase family.

Sequence caution

The sequence ABK75957.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 762762Multifunctional non-homologous end joining protein LigD
PRO_0000425949

Regions

DNA binding18 – 214 By similarity
DNA binding311 By similarity
DNA binding58 – 603 By similarity
DNA binding68 – 725 By similarity
DNA binding761 By similarity
DNA binding88 – 936 By similarity
DNA binding1091 By similarity
Nucleotide binding136 – 1383Substrate; for polymerase activity By similarity
Nucleotide binding171 – 1777Substrate; for polymerase activity By similarity
DNA binding233 – 2342 By similarity
Region14 – 260247DNA repair polymerase domain (Pol)
Region296 – 4531583'-phosphoesterase domain (PE)
Region463 – 760298Ligase domain (Lig)

Sites

Active site4841N6-AMP-lysine intermediate Probable
Metal binding1361Manganese 1 By similarity
Metal binding1361Manganese 2 By similarity
Metal binding1381Manganese 1 By similarity
Metal binding1381Manganese 2 By similarity
Metal binding2261Manganese 2 By similarity
Metal binding3301Manganese 3; catalytic; via pros nitrogen; for 3'-phosphoesterase activity By similarity
Metal binding3361Manganese 3; catalytic; via tele nitrogen; for 3'-phosphoesterase activity By similarity
Metal binding3381Manganese 3; catalytic; for 3'-phosphoesterase activity By similarity
Metal binding4861Manganese 4 By similarity
Metal binding6161Manganese 4 By similarity
Binding site571Substrate; for polymerase activity By similarity
Binding site1161Substrate; for polymerase activity By similarity
Binding site2291Substrate; for polymerase activity By similarity
Binding site2351Substrate; for polymerase activity By similarity
Binding site2431Substrate; for polymerase activity By similarity
Site3721Transition state stabilizer; for 3'-phosphoesterase activity By similarity

Experimental info

Mutagenesis136 – 1383DLD → 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. Ref.4 Ref.6 Ref.7 Ref.11
Mutagenesis1361D → A: Loss of templated and non-templated DNA synthesis, but not ligase activity. Ref.4
Mutagenesis1381D → A: Loss of templated and non-templated DNA synthesis, but not ligase activity. Ref.4
Mutagenesis3101E → A: No effect on efficiency or fidelity on NHEJ of blunt, 5'-overhangs or 3'-overhangs. Ref.11
Mutagenesis3361H → A: No effect on efficiency or fidelity on NHEJ of blunt, 5'-overhangs or 3'-overhangs. Ref.11
Mutagenesis4841K → 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. Ref.5 Ref.6 Ref.11
Mutagenesis5331E → 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. Ref.11

Sequences

Sequence LengthMass (Da)Tools
A0R3R7 [UniParc].

Last modified March 19, 2014. Version 2.
Checksum: ED1853A73A3E552E

FASTA76285,516
        10         20         30         40         50         60 
MARHPWGMER YERVRLTNPD KVLYPATGTT KAEVFDYYLS IAQVMVPHIA GRPVTRKRWP 

        70         80         90        100        110        120 
NGVAEEAFFE KQLASSAPSW LERGSITHKS GTTTYPIINT REGLAWVAQQ ASLEVHVPQW 

       130        140        150        160        170        180 
RFEDGDQGPA TRIVFDLDPG EGVTMTQLCE IAHEVRALMT DLDLETYPLT SGSKGLHLYV 

       190        200        210        220        230        240 
PLAEPISSRG ASVLARRVAQ QLEQAMPKLV TATMTKSLRA GKVFLDWSQN NAAKTTIAPY 

       250        260        270        280        290        300 
SLRGRDHPTV AAPRTWDEIA DPELRHLRFD EVLDRLDEYG DLLAPLDADA PIADKLTTYR 

       310        320        330        340        350        360 
SMRDASKTPE PVPKEIPKTG NNDKFVIQEH HARRLHYDLR LERDGVLVSF AVPKNLPETT 

       370        380        390        400        410        420 
AENRLAVHTE DHPIEYLAFH GSIPKGEYGA GDMVIWDSGS YETEKFRVPE ELDNPDDSHG 

       430        440        450        460        470        480 
EIIVTLHGEK VDGRYALIQT KGKNWLAHRM KDQKNARPED FAPMLATEGS VAKYKAKQWA 

       490        500        510        520        530        540 
FEGKWDGYRV IIDADHGQLQ IRSRTGREVT GEYPQFKALA ADLAEHHVVL DGEAVALDES 

       550        560        570        580        590        600 
GVPSFGQMQN RARSTRVEFW AFDILWLDGR SLLRAKYSDR RKILEALADG GGLIVPDQLP 

       610        620        630        640        650        660 
GDGPEAMEHV RKKRFEGVVA KKWDSTYQPG RRSSSWIKDK IWNTQEVVIG GWRQGEGGRS 

       670        680        690        700        710        720 
SGIGALVLGI PGPEGLQFVG RVGTGFTEKE LSKLKDMLKP LHTDESPFNA PLPKVDARGV 

       730        740        750        760 
TFVRPELVGE VRYSERTSDG RLRQPSWRGL RPDKTPDEVV WE 

« Hide

References

« Hide 'large scale' references
[1]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
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 700084 / mc(2)155.
[2]"Interrupted coding sequences in Mycobacterium smegmatis: authentic mutations or sequencing errors?"
Deshayes C., Perrodou E., Gallien S., Euphrasie D., Schaeffer C., Van-Dorsselaer A., Poch O., Lecompte O., Reyrat J.-M.
Genome Biol. 8:R20.1-R20.9(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 700084 / mc(2)155.
[3]"Ortho-proteogenomics: multiple proteomes investigation through orthology and a new MS-based protocol."
Gallien S., Perrodou E., Carapito C., Deshayes C., Reyrat J.-M., Van Dorsselaer A., Poch O., Schaeffer C., Lecompte O.
Genome Res. 19:128-135(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 700084 / mc(2)155.
[4]"Mechanism of nonhomologous end-joining in mycobacteria: a low-fidelity repair system driven by Ku, ligase D and ligase C."
Gong C., Bongiorno P., Martins A., Stephanou N.C., Zhu H., Shuman S., Glickman M.S.
Nat. Struct. Mol. Biol. 12:304-312(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, DISRUPTION PHENOTYPE, MUTAGENESIS OF ASP-136 AND ASP-138.
Strain: ATCC 700084 / mc(2)155.
[5]"Crystal structure and nonhomologous end-joining function of the ligase component of Mycobacterium DNA ligase D."
Akey D., Martins A., Aniukwu J., Glickman M.S., Shuman S., Berger J.M.
J. Biol. Chem. 281:13412-13423(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, PROBABLE ACTIVE SITE, MUTAGENESIS OF LYS-484.
Strain: ATCC 700084 / mc(2)155.
[6]"Mycobacteriophage exploit NHEJ to facilitate genome circularization."
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.
Mol. Cell 23:743-748(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN VIRAL REPLICATION, INTERACTION WITH VIRAL KU HOMOLOGS, DISRUPTION PHENOTYPE, MUTAGENESIS OF 136-ASP--ASP-138 AND LYS-484.
Strain: ATCC 700084 / mc(2)155.
[7]"Atomic structure and nonhomologous end-joining function of the polymerase component of bacterial DNA ligase D."
Zhu H., Nandakumar J., Aniukwu J., Wang L.K., Glickman M.S., Lima C.D., Shuman S.
Proc. Natl. Acad. Sci. U.S.A. 103:1711-1716(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, MUTAGENESIS OF 136-ASP--ASP-138.
[8]"NHEJ protects mycobacteria in stationary phase against the harmful effects of desiccation."
Pitcher R.S., Green A.J., Brzostek A., Korycka-Machala M., Dziadek J., Doherty A.J.
DNA Repair 6:1271-1276(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, DISRUPTION PHENOTYPE.
Strain: ATCC 700084 / mc(2)155.
[9]"Mycobacterial nonhomologous end joining mediates mutagenic repair of chromosomal double-strand DNA breaks."
Stephanou N.C., Gao F., Bongiorno P., Ehrt S., Schnappinger D., Shuman S., Glickman M.S.
J. Bacteriol. 189:5237-5246(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: DISRUPTION PHENOTYPE.
Strain: ATCC 700084 / mc(2)155.
[10]"Structure and function of a mycobacterial NHEJ DNA repair polymerase."
Pitcher R.S., Brissett N.C., Picher A.J., Andrade P., Juarez R., Thompson D., Fox G.C., Blanco L., Doherty A.J.
J. Mol. Biol. 366:391-405(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN GAP FILLING, COFACTOR, DOMAIN, DNA-BINDING.
[11]"The pathways and outcomes of mycobacterial NHEJ depend on the structure of the broken DNA ends."
Aniukwu J., Glickman M.S., Shuman S.
Genes Dev. 22:512-527(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, DOMAIN, DISRUPTION PHENOTYPE, MUTAGENESIS OF 136-ASP--ASP-138; GLU-310; HIS-336; LYS-484 AND GLU-533.
Strain: ATCC 700084 / mc(2)155.
[12]"Mycobacteria exploit three genetically distinct DNA double-strand break repair pathways."
Gupta R., Barkan D., Redelman-Sidi G., Shuman S., Glickman M.S.
Mol. Microbiol. 79:316-330(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: DISRUPTION PHENOTYPE.
Strain: ATCC 700084 / mc(2)155.
[13]"A Sir2-like protein participates in mycobacterial NHEJ."
Li Z., Wen J., Lin Y., Wang S., Xue P., Zhang Z., Zhou Y., Wang X., Sui L., Bi L.J., Zhang X.E.
PLoS ONE 6:E20045-E20045(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH SIR2, SUBUNIT.
Strain: ATCC 700084 / mc(2)155.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP000480 Genomic DNA. Translation: ABK75957.1. Different initiation.
CP001663 Genomic DNA. Translation: AFP41860.1.
RefSeqYP_006570155.1. NC_018289.1.
YP_889805.1. NC_008596.1.

3D structure databases

ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING246196.MSMEG_5570.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaABK75957; ABK75957; MSMEG_5570.
GeneID4535131.
KEGGmsm:MSMEG_5570.
PATRIC18083411. VBIMycSme59918_5431.

Phylogenomic databases

eggNOGCOG3285.
HOGENOMHOG000222509.
KOK01971.
OMASKGIHLY.
OrthoDBEOG661H49.

Enzyme and pathway databases

BioCycMSME246196:GJ4Y-5569-MONOMER.

Family and domain databases

Gene3D2.40.50.140. 1 hit.
InterProIPR012309. DNA_ligase_ATP-dep_C.
IPR012310. DNA_ligase_ATP-dep_cent.
IPR014146. DNA_pol_LigD_ligase_dom.
IPR002755. DNA_primase_S.
IPR014144. LigD_PE_domain.
IPR014145. LigD_pol.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PfamPF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF01896. DNA_primase_S. 1 hit.
PF13298. LigD_N. 1 hit.
[Graphical view]
SUPFAMSSF50249. SSF50249. 1 hit.
TIGRFAMsTIGR02777. LigD_PE_dom. 1 hit.
TIGR02778. ligD_pol. 1 hit.
TIGR02779. NHEJ_ligase_lig. 1 hit.
PROSITEPS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameLIGD_MYCS2
AccessionPrimary (citable) accession number: A0R3R7
Secondary accession number(s): I7FKR9
Entry history
Integrated into UniProtKB/Swiss-Prot: March 19, 2014
Last sequence update: March 19, 2014
Last modified: July 9, 2014
This is version 57 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families