Multifunctional non-homologous end joining DNA repair protein LigD - P9WNV3 (LIGD_MYCTU)

 

Protein Feature View of PDB entries mapped to a UniProtKB sequence  

  • Number of PDB entries for P9WNV3: 7
 
Function
With Ku forms a non-homologous end joining (NHEJ) repair enzyme which repairs DNA double-strand breaks (DSB) with reduced fidelity. Recognizes, processes and reseals DSBs, including repairs on incompatible DSB which require 3'-resection, gap filling and ligation. Anneals the 3' overhanging strands from opposing breaks to form a gapped intermediate, which then can be extended in trans by using the termini as primers for extension of the annealed break. Binds to the recessed 5'-phosphate moiety of the downstream DNA strand forming a stable synaptic complex even when the 3'-protruding ends of the template DNA strands are not complementary. Has numerous activites; gap filling copies the template strand, and prefers a 5'-phosphate in the gap and rNTPS (PubMed:17174332, PubMed:17947582), DNA-directed DNA or RNA polymerase on 5'-overhangs, terminal transferase (extending ssDNA or blunt dsDNA in a non-templated fashion, preferentially with rNTPs), DNA-dependent RNA primase (synthesizes short RNAs on unprimed closed ssDNA) and 3'- to 5'-exonuclease on ssDNA (PubMed:15499016). Isolated Pol domain (and presumably the holoenzyme) is able to form complexes between 2 noncompatible protruding 3'-ends DNA ends via microhomologous DNA strands, in a end-bridging function to which it adds a templated nucleotide (PubMed:17947582). Minimal primer length is 2 nucleotides (PubMed:21255731). UniProt
Catalytic Activity
ATP + deoxyribonucleotiden + deoxyribonucleotidem = AMP + diphosphate + deoxyribonucleotiden+m. UniProt
Pathway Maps
Maps:       
Reactions:
      ESCHER  BiGG
Subunit Structure
Monomer. Component of the NHEJ repair enzyme with mKu. Interacts with Ku in the absence of DSB via the Pol domain. In structures of the Pol domain with template DNA 2 Pol domains are bound to microhomologous DNA complexes to form an end-bridging complex. Probably interacts with Mycobacterium phage Omega and Corndog Ku homologs (AC Q853W0, AC Q856K7). Interacts with Sir2; may form a trimeric complex with LigD during NHEJ. UniProt
Domain
The C-terminal ligase domain (Lig) binds dsDNA and functions as an independent domain (PubMed:14985346, PubMed:16023671). UniProt
  • Other Gene names: ligD, Rv0938, MTCY08D9.01c, MTCY10D7.36c
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Data in green originates from UniProtKB  
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Data in yellow originates from Pfam  , by interacting with the HMMER3 web site  
Data in purple originates from Phosphosite  .
Data in orange originates from the SCOP   (version 1.75) and SCOPe   (version 2.04) classifications.
Data in grey has been calculated using BioJava  . Protein disorder predictions are based on JRONN (Troshin, P. and Barton, G. J. unpublished), a Java implementation of RONN  
  • Red: potentially disorderd region
  • Blue: probably ordered region.
Hydropathy has been calculated using a sliding window of 15 residues and summing up scores from standard hydrophobicity tables.
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  • Blue: hydrophilic.
Data in lilac represent the genomic exon structure projected onto the UniProt sequence.
Data in blue originates from PDB
  • Secstruc: Secondary structure projected from representative PDB entries onto the UniProt sequence.
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The PDB to UniProt mapping is based on the data provided by the EBI SIFTS project. See also Velankar et al., Nucleic Acids Research 33, D262-265 (2005).
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