TB Genome Annotation Portal

Rv0938 (ligD)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: DNA ligase D
  • REFSEQ: ATP-dependent DNA ligase
  • PATRIC: ATP-dependent DNA ligase (EC 6.5.1.1) clustered with Ku protein LigD
  • TUBERCULIST: ATP dependent DNA ligase LigD (ATP dependent polydeoxyribonucleotide synthase) (thermostable DNA ligase) (ATP dependent polynucleotide ligase) (sealase) (DNA repair enzyme) (DNA joinase)
  • NCBI: ATP dependent DNA ligase LigD (ATP dependent polydeoxyribonucleotide synthase) (thermostable DNA ligase) (ATP dependent polynucleotide ligase) (sealase) (DNA repair enzyme) (DNA joinase)
  • updated information (H37Rv4):
    • gene name: ligD
    • function:
    • reference:
• Type: Not Target
• Start: 1046136
• End: 1048415
• Operon:


• Trans-membrane region:
  
• Role: V - Conserved hypotheticals
• GO terms:
  • GO:0090305 - nucleic acid phosphodiester bond hydrolysis (Uniprot)
  • GO:0071897 - DNA biosynthetic process (Uniprot)
  • GO:0046872 - metal ion binding (Uniprot)
  • GO:0030145 - manganese ion binding (Uniprot)
  • GO:0016874 - ligase activity (Uniprot)
  • GO:0016787 - hydrolase activity (Uniprot)
  • GO:0016779 - nucleotidyltransferase activity (Uniprot)
  • GO:0016740 - transferase activity (Uniprot)
  • GO:0016032 - viral process (Uniprot)
  • GO:0008310 - single-stranded DNA 3'-5' exodeoxyribonuclease activity (Uniprot)
  • GO:0008152 - metabolic process (Uniprot)
  • GO:0006974 - cellular response to DNA damage stimulus (Uniprot)
  • GO:0006310 - DNA recombination (Uniprot)
  • GO:0006303 - double-strand break repair via nonhomologous end joining (Uniprot)
  • GO:0006281 - DNA repair (Uniprot)
  • GO:0006269 - DNA replication, synthesis of RNA primer (Uniprot)
  • GO:0006266 - DNA ligation (Uniprot)
  • GO:0005886 - plasma membrane (Uniprot)
  • GO:0005524 - ATP binding (Uniprot)
  • GO:0005515 - protein binding (Uniprot)
  • GO:0004652 - polynucleotide adenylyltransferase activity (Uniprot)
  • GO:0004527 - exonuclease activity (Uniprot)
  • GO:0004518 - nuclease activity (Uniprot)
  • GO:0003910 - DNA ligase (ATP) activity (Uniprot)
  • GO:0003909 - DNA ligase activity (Uniprot)
  • GO:0003899 - DNA-directed 5'-3' RNA polymerase activity (Uniprot)
  • GO:0003896 - DNA primase activity (Uniprot)
  • GO:0003887 - DNA-directed DNA polymerase activity (Uniprot)
  • GO:0003824 - catalytic activity (Uniprot)
  • GO:0003677 - DNA binding (Uniprot)
  • GO:0000287 - magnesium ion binding (Uniprot)
  • GO:0000166 - nucleotide binding (Uniprot)
• Reaction(s) (based on iSM810 metabolic model):
• Gene Expression Profile (Transcriptional Responses to Drugs; Boshoff et al, 2004)
• Gene Modules extracted from cluster analysis of 249 transcriptomic datasets using ICA
• Orthologs among selected mycobacteria
• Protein structure: 2iru, 2r9l, 2irx, 2iry, 3pky, 1vs0
• Search for Homologs in PDB
• Top 10 Homologs in PDB (as of Nov 2020):
  

  PDB	aa ident	species	PDB title
  4MKY	100%	Mycobacterium tuberculosis	Polymerase Domain from Mycobacterium tuberculosis Ligase D in complex with an annealed double-strand DNA break.
  3PKY	100%	Mycobacterium tuberculosis	Polymerase Domain from Mycobacterium tuberculosis Ligase D in complex with DNA, UTP and Manganese.
  2R9L	100%	Mycobacterium tuberculosis H37Rv	Polymerase Domain from Mycobacterium tuberculosis Ligase D in complex with DNA
  2IRY	100%	Mycobacterium tuberculosis	Crystal Structure of the Polymerase Domain from Mycobacterium tuberculosis Ligase D with dGTP and Manganese.
  2IRX	100%	Mycobacterium tuberculosis	Crystal Structure of the Polymerase Domain from Mycobacterium tuberculosis Ligase D with GTP and Manganese.
  2IRU	100%	Mycobacterium tuberculosis	Crystal Structure of the Polymerase Domain from Mycobacterium tuberculosis Ligase D
  1VS0	100%	Mycobacterium tuberculosis	Crystal Structure of the Ligase Domain from M. tuberculosis LigD at 2.4A
  6NHZ	99%	Mycobacterium tuberculosis	mycobacterial DNA ligase D complexed with ATP and Mg
  6NHX	98%	Mycobacterium tuberculosis	mycobacterial DNA ligase D complexed with ATP and MES
  3P43	53%	Methanosarcina barkeri str. Fusaro	Structure and Activities of Archaeal Members of the LigD 3' Phosphoesterase DNA Repair Enzyme Superfamily

• Links to additional information on ligD:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 1.248 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

MGSASEQRVTLTNADKVLYPATGTTKSDIFDYYAGVAEVMLGHIAGRPATRKRWPNGVDQPAFFEKQLALSAPPWLSRATVAHRSGTTTYPIIDSATGLA
WIAQQAALEVHVPQWRFVAEPGSGELNPGPATRLVFDLDPGEGVMMAQLAEVARAVRDLLADIGLVTFPVTSGSKGLHLYTPLDEPVSSRGATVLAKRVA
QRLEQAMPALVTSTMTKSLRAGKVFVDWSQNSGSKTTIAPYSLRGRTHPTVAAPRTWAELDDPALRQLSYDEVLTRIARDGDLLERLDADAPVADRLTRY
RRMRDASKTPEPIPTAKPVTGDGNTFVIQEHHARRPHYDFRLECDGVLVSWAVPKNLPDNTSVNHLAIHTEDHPLEYATFEGAIPSGEYGAGKVIIWDSG
TYDTEKFHDDPHTGEVIVNLHGGRISGRYALIRTNGDRWLAHRLKNQKDQKVFEFDNLAPMLATHGTVAGLKASQWAFEGKWDGYRLLVEADHGAVRLRS
RSGRDVTAEYPQLRALAEDLADHHVVLDGEAVVLDSSGVPSFSQMQNRGRDTRVEFWAFDLLYLDGRALLGTRYQDRRKLLETLANATSLTVPELLPGDG
AQAFACSRKHGWEGVIAKRRDSRYQPGRRCASWVKDKHWNTQEVVIGGWRAGEGGRSSGVGSLLMGIPGPGGLQFAGRVGTGLSERELANLKEMLAPLHT
DESPFDVPLPARDAKGITYVKPALVAEVRYSEWTPEGRLRQSSWRGLRPDKKPSEVVRE

Additional Information

Analysis of Positive Selection in Clinical Isolates *new*

• Analysis of dN/dS (omega) in two collections of Mtb clinical isolates using GenomegaMap (Window model) (see description of methods)
  • Moldova: 2,057 clinical isolates
  • global set: 5,195 clinical isolates from 15 other countries
• In the omega plots, the black line shows the mean estimate of omega (dN/dS) at each codon, and the blue lines are the bounds for the 95% credible interval (95%CI, from MCMC sampling).
• A gene is under significant positive selection if the lower-bound of the 95%CI of omega (lower blue line) exceeds 1.0 at any codon.

	Moldova (2,057)	global set (5,195)
under significant positive selection?	NO	NO
omega peak height (95%CI lower bound)	1.68 (0.25)	1.35 (0.5)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link