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A0R3R7

- LIGD_MYCS2

UniProt

A0R3R7 - LIGD_MYCS2

Protein

Multifunctional non-homologous end joining protein LigD

Gene

ligD

Organism
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 59 (01 Oct 2014)
      Sequence version 2 (19 Mar 2014)
      Previous versions | rss
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    Functioni

    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.
    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
    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 activityi

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

    Cofactori

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

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei57 – 571Substrate; for polymerase activityBy similarity
    Binding sitei116 – 1161Substrate; for polymerase activityBy similarity
    Metal bindingi136 – 1361Manganese 1By similarity
    Metal bindingi136 – 1361Manganese 2By similarity
    Metal bindingi138 – 1381Manganese 1By similarity
    Metal bindingi138 – 1381Manganese 2By similarity
    Metal bindingi226 – 2261Manganese 2By similarity
    Binding sitei229 – 2291Substrate; for polymerase activityBy similarity
    Binding sitei235 – 2351Substrate; for polymerase activityBy similarity
    Binding sitei243 – 2431Substrate; for polymerase activityBy similarity
    Metal bindingi330 – 3301Manganese 3; catalytic; via pros nitrogen; for 3'-phosphoesterase activityBy similarity
    Metal bindingi336 – 3361Manganese 3; catalytic; via tele nitrogen; for 3'-phosphoesterase activityBy similarity
    Metal bindingi338 – 3381Manganese 3; catalytic; for 3'-phosphoesterase activityBy similarity
    Sitei372 – 3721Transition state stabilizer; for 3'-phosphoesterase activityBy similarity
    Active sitei484 – 4841N6-AMP-lysine intermediateCurated
    Metal bindingi486 – 4861Manganese 4By similarity
    Metal bindingi616 – 6161Manganese 4By similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    DNA bindingi18 – 214By similarity
    DNA bindingi31 – 311By similarity
    DNA bindingi58 – 603By similarity
    DNA bindingi68 – 725By similarity
    DNA bindingi76 – 761By similarity
    DNA bindingi88 – 936By similarity
    DNA bindingi109 – 1091By similarity
    Nucleotide bindingi136 – 1383Substrate; for polymerase activityBy similarity
    Nucleotide bindingi171 – 1777Substrate; for polymerase activityBy similarity
    DNA bindingi233 – 2342By similarity

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-KW
    2. DNA binding Source: UniProtKB-KW
    3. DNA-directed DNA polymerase activity Source: UniProtKB-KW
    4. DNA ligase (ATP) activity Source: UniProtKB-EC
    5. DNA primase activity Source: InterPro
    6. exonuclease activity Source: UniProtKB-KW
    7. metal ion binding Source: UniProtKB-KW

    GO - Biological processi

    1. DNA recombination Source: UniProtKB-KW
    2. double-strand break repair via nonhomologous end joining Source: UniProtKB
    3. viral process Source: UniProtKB-KW

    Keywords - Molecular functioni

    DNA-directed DNA polymerase, Exonuclease, Hydrolase, Ligase, Nuclease, Nucleotidyltransferase, Transferase

    Keywords - Biological processi

    DNA damage, DNA recombination, DNA repair, Host-virus interaction

    Keywords - Ligandi

    ATP-binding, DNA-binding, Manganese, Metal-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciMSME246196:GJ4Y-5569-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Multifunctional non-homologous end joining protein LigD
    Alternative name(s):
    NHEJ DNA polymerase
    Including the following 3 domains:
    DNA repair polymerase
    Short name:
    Pol
    Alternative name(s):
    Polymerase/primase
    3'-phosphoesterase
    Short name:
    3'-ribonuclease/3'-phosphatase
    Short name:
    PE
    DNA ligase (EC:6.5.1.1)
    Short name:
    Lig
    Alternative name(s):
    Polydeoxyribonucleotide synthase [ATP]
    Gene namesi
    Name:ligD
    Ordered Locus Names:MSMEG_5570, MSMEI_5419
    OrganismiMycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
    Taxonomic identifieri246196 [NCBI]
    Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeMycobacteriaceaeMycobacterium
    ProteomesiUP000000757: Chromosome, UP000006158: Chromosome

    Pathology & Biotechi

    Disruption phenotypei

    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.6 Publications

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi136 – 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. 2 Publications
    Mutagenesisi136 – 1361D → A: Loss of templated and non-templated DNA synthesis, but not ligase activity. 2 Publications
    Mutagenesisi138 – 1381D → A: Loss of templated and non-templated DNA synthesis, but not ligase activity. 2 Publications
    Mutagenesisi310 – 3101E → A: No effect on efficiency or fidelity on NHEJ of blunt, 5'-overhangs or 3'-overhangs. 2 Publications
    Mutagenesisi336 – 3361H → A: No effect on efficiency or fidelity on NHEJ of blunt, 5'-overhangs or 3'-overhangs. 2 Publications
    Mutagenesisi484 – 4841K → 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. 4 Publications
    Mutagenesisi533 – 5331E → 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. 2 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 762762Multifunctional non-homologous end joining protein LigDPRO_0000425949Add
    BLAST

    Interactioni

    Subunit structurei

    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).2 Publications

    Protein-protein interaction databases

    STRINGi246196.MSMEG_5570.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni14 – 260247DNA repair polymerase domain (Pol)Add
    BLAST
    Regioni296 – 4531583'-phosphoesterase domain (PE)Add
    BLAST
    Regioni463 – 760298Ligase domain (Lig)Add
    BLAST

    Domaini

    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).2 Publications
    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).2 Publications
    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).2 Publications

    Sequence similaritiesi

    In the N-terminal section; belongs to the LigD polymerase family.Curated
    In the central section; belongs to the LigD 3'-phosphoesterase family.Curated
    In the C-terminal section; belongs to the ATP-dependent DNA ligase family.Curated

    Phylogenomic databases

    eggNOGiCOG3285.
    HOGENOMiHOG000222509.
    KOiK01971.
    OMAiSKGIHLY.
    OrthoDBiEOG661H49.

    Family and domain databases

    Gene3Di2.40.50.140. 1 hit.
    InterProiIPR012309. 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]
    PfamiPF04679. 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]
    SUPFAMiSSF50249. SSF50249. 1 hit.
    TIGRFAMsiTIGR02777. LigD_PE_dom. 1 hit.
    TIGR02778. ligD_pol. 1 hit.
    TIGR02779. NHEJ_ligase_lig. 1 hit.
    PROSITEiPS50160. DNA_LIGASE_A3. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    A0R3R7-1 [UniParc]FASTAAdd to Basket

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    MARHPWGMER YERVRLTNPD KVLYPATGTT KAEVFDYYLS IAQVMVPHIA    50
    GRPVTRKRWP NGVAEEAFFE KQLASSAPSW LERGSITHKS GTTTYPIINT 100
    REGLAWVAQQ ASLEVHVPQW RFEDGDQGPA TRIVFDLDPG EGVTMTQLCE 150
    IAHEVRALMT DLDLETYPLT SGSKGLHLYV PLAEPISSRG ASVLARRVAQ 200
    QLEQAMPKLV TATMTKSLRA GKVFLDWSQN NAAKTTIAPY SLRGRDHPTV 250
    AAPRTWDEIA DPELRHLRFD EVLDRLDEYG DLLAPLDADA PIADKLTTYR 300
    SMRDASKTPE PVPKEIPKTG NNDKFVIQEH HARRLHYDLR LERDGVLVSF 350
    AVPKNLPETT AENRLAVHTE DHPIEYLAFH GSIPKGEYGA GDMVIWDSGS 400
    YETEKFRVPE ELDNPDDSHG EIIVTLHGEK VDGRYALIQT KGKNWLAHRM 450
    KDQKNARPED FAPMLATEGS VAKYKAKQWA FEGKWDGYRV IIDADHGQLQ 500
    IRSRTGREVT GEYPQFKALA ADLAEHHVVL DGEAVALDES GVPSFGQMQN 550
    RARSTRVEFW AFDILWLDGR SLLRAKYSDR RKILEALADG GGLIVPDQLP 600
    GDGPEAMEHV RKKRFEGVVA KKWDSTYQPG RRSSSWIKDK IWNTQEVVIG 650
    GWRQGEGGRS SGIGALVLGI PGPEGLQFVG RVGTGFTEKE LSKLKDMLKP 700
    LHTDESPFNA PLPKVDARGV TFVRPELVGE VRYSERTSDG RLRQPSWRGL 750
    RPDKTPDEVV WE 762
    Length:762
    Mass (Da):85,516
    Last modified:March 19, 2014 - v2
    Checksum:iED1853A73A3E552E
    GO

    Sequence cautioni

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

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000480 Genomic DNA. Translation: ABK75957.1. Different initiation.
    CP001663 Genomic DNA. Translation: AFP41860.1.
    RefSeqiWP_014878386.1. NC_018289.1.
    YP_006570155.1. NC_018289.1.
    YP_889805.1. NC_008596.1.

    Genome annotation databases

    EnsemblBacteriaiABK75957; ABK75957; MSMEG_5570.
    GeneIDi4535131.
    KEGGimsg:MSMEI_5419.
    msm:MSMEG_5570.
    PATRICi18083411. VBIMycSme59918_5431.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000480 Genomic DNA. Translation: ABK75957.1 . Different initiation.
    CP001663 Genomic DNA. Translation: AFP41860.1 .
    RefSeqi WP_014878386.1. NC_018289.1.
    YP_006570155.1. NC_018289.1.
    YP_889805.1. NC_008596.1.

    3D structure databases

    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 246196.MSMEG_5570.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ABK75957 ; ABK75957 ; MSMEG_5570 .
    GeneIDi 4535131.
    KEGGi msg:MSMEI_5419.
    msm:MSMEG_5570.
    PATRICi 18083411. VBIMycSme59918_5431.

    Phylogenomic databases

    eggNOGi COG3285.
    HOGENOMi HOG000222509.
    KOi K01971.
    OMAi SKGIHLY.
    OrthoDBi EOG661H49.

    Enzyme and pathway databases

    BioCyci MSME246196:GJ4Y-5569-MONOMER.

    Family and domain databases

    Gene3Di 2.40.50.140. 1 hit.
    InterProi IPR012309. 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 ]
    Pfami PF04679. 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 ]
    SUPFAMi SSF50249. SSF50249. 1 hit.
    TIGRFAMsi TIGR02777. LigD_PE_dom. 1 hit.
    TIGR02778. ligD_pol. 1 hit.
    TIGR02779. NHEJ_ligase_lig. 1 hit.
    PROSITEi PS50160. DNA_LIGASE_A3. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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. 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. 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.

    Entry informationi

    Entry nameiLIGD_MYCS2
    AccessioniPrimary (citable) accession number: A0R3R7
    Secondary accession number(s): I7FKR9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 19, 2014
    Last sequence update: March 19, 2014
    Last modified: October 1, 2014
    This is version 59 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

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

    Keywords - Technical termi

    Complete proteome, Multifunctional enzyme, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3