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A0R3R7

- LIGD_MYCS2

UniProt

A0R3R7 - LIGD_MYCS2

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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

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
Complete GO annotation...

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. 3 Publications
Mutagenesisi136 – 1361D → A: Loss of templated and non-templated DNA synthesis, but not ligase activity. 1 Publication
Mutagenesisi138 – 1381D → A: Loss of templated and non-templated DNA synthesis, but not ligase activity. 1 Publication
Mutagenesisi310 – 3101E → A: No effect on efficiency or fidelity on NHEJ of blunt, 5'-overhangs or 3'-overhangs. 1 Publication
Mutagenesisi336 – 3361H → A: No effect on efficiency or fidelity on NHEJ of blunt, 5'-overhangs or 3'-overhangs. 1 Publication
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. 3 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. 1 Publication

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

« Hide

        10         20         30         40         50
MARHPWGMER YERVRLTNPD KVLYPATGTT KAEVFDYYLS IAQVMVPHIA
60 70 80 90 100
GRPVTRKRWP NGVAEEAFFE KQLASSAPSW LERGSITHKS GTTTYPIINT
110 120 130 140 150
REGLAWVAQQ ASLEVHVPQW RFEDGDQGPA TRIVFDLDPG EGVTMTQLCE
160 170 180 190 200
IAHEVRALMT DLDLETYPLT SGSKGLHLYV PLAEPISSRG ASVLARRVAQ
210 220 230 240 250
QLEQAMPKLV TATMTKSLRA GKVFLDWSQN NAAKTTIAPY SLRGRDHPTV
260 270 280 290 300
AAPRTWDEIA DPELRHLRFD EVLDRLDEYG DLLAPLDADA PIADKLTTYR
310 320 330 340 350
SMRDASKTPE PVPKEIPKTG NNDKFVIQEH HARRLHYDLR LERDGVLVSF
360 370 380 390 400
AVPKNLPETT AENRLAVHTE DHPIEYLAFH GSIPKGEYGA GDMVIWDSGS
410 420 430 440 450
YETEKFRVPE ELDNPDDSHG EIIVTLHGEK VDGRYALIQT KGKNWLAHRM
460 470 480 490 500
KDQKNARPED FAPMLATEGS VAKYKAKQWA FEGKWDGYRV IIDADHGQLQ
510 520 530 540 550
IRSRTGREVT GEYPQFKALA ADLAEHHVVL DGEAVALDES GVPSFGQMQN
560 570 580 590 600
RARSTRVEFW AFDILWLDGR SLLRAKYSDR RKILEALADG GGLIVPDQLP
610 620 630 640 650
GDGPEAMEHV RKKRFEGVVA KKWDSTYQPG RRSSSWIKDK IWNTQEVVIG
660 670 680 690 700
GWRQGEGGRS SGIGALVLGI PGPEGLQFVG RVGTGFTEKE LSKLKDMLKP
710 720 730 740 750
LHTDESPFNA PLPKVDARGV TFVRPELVGE VRYSERTSDG RLRQPSWRGL
760
RPDKTPDEVV WE
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.
RefSeqiYP_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 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

« Hide 'large scale' publications
  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 29, 2014
This is version 60 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