HMM Summary Page: TIGR02776

FunctionDNA ligase D
Gene SymbolligD
Trusted Cutoff373.20
Domain Trusted Cutoff373.20
Noise Cutoff221.10
Domain Noise Cutoff221.10
Isology Typeequivalog
HMM Length587
Mainrole CategoryDNA metabolism
Subrole CategoryDNA replication, recombination, and repair
Gene Ontology TermGO:0006303: double-strand break repair via nonhomologous end joining biological_process
AuthorHaft DH
Entry DateJan 10 2006 10:00AM
Last ModifiedFeb 14 2011 3:27PM
CommentMembers of this protein family are DNA ligases involved in the repair of DNA double-stranded breaks by non-homologous end joining (NHEJ). The system of the bacterial Ku protein (TIGR02772) plus this DNA ligase is seen in about 20 % of bacterial genomes to date and at least one archaeon (Archeoglobus fulgidus). This model describes a central and a C-terminal domain. These two domains may be permuted, as in genus Mycobacterium, or divided into tandem ORFs, and therefore not be identified by this HMM. An additional N-terminal 3'-phosphoesterase (PE) domain present in some but not all examples of this ligase is not included in the seed alignment for this model; this HMM models only the central ATP-dependent ligase domain and the C-terminal polymerase domain. Most examples of genes for this ligase are adjacent to the gene for Ku.
ReferencesRN [1] RM 16046407 RT Essential constituents of the 3'-phosphoesterase domain of bacterial DNA ligase D, a nonhomologous end-joining enzyme. RA Zhu H, Wang LK, Shuman S. RL J Biol Chem. 2005 Oct 7;280(40):33707-15.