The amino-terminal module of the poxvirus D6R/NIR proteins defines a novel conserved DNA-binding domain (the KilA-N domain) that is found in a wide range of proteins of large bacterial and eukaryotic DNA viruses [ (PUBMED:11897024) ]. Putative proteins with homology to the KilA-N domain have also been identified in Maverick transposable elements of the parabasalid protozoa Trichomonas vaginalis [ (PUBMED:17034960) ]. The KilA-N domain has been suggested to be homologous to the fungal DNA-binding APSES domain. In all proteins shown to contain the KilA-N domain, it occurs at the extreme amino terminus accompanied by a wide range of distinct carboxy-terminal domains. These carboxy-terminal modules may be enzymes, such as the nuclease domains, or might mediate additional, specific interactions with nucleic acids or proteins, like the RING or CCCH fingers in the poxviruses [ (PUBMED:11897024) ]. The KilA-N domain is predicted to adopt an alpha-beta fold with four conserved strands and at least two conserved helices [ (PUBMED:11897024) ]. Some proteins known to contain a KilA-N domain are listed below:
Extensive domain shuffling in transcription regulators of DNA viruses andimplications for the origin of fungal APSES transcription factors.
Genome Biol. 2002; 3: 12-12
Display abstract
BACKGROUND: Viral DNA-binding proteins have served as good models to studythe biochemistry of transcription regulation and chromatin dynamics.Computational analysis of viral DNA-binding regulatory proteins andidentification of their previously undetected homologs encoded by cellulargenomes might lead to a better understanding of their function andevolution in both viral and cellular systems. RESULTS: The phyletic rangeand the conserved DNA-binding domains of the viral regulatory proteins ofthe poxvirus D6R/N1R and baculoviral Bro protein families have not beenpreviously defined. Using computational analysis, we show that theamino-terminal module of the D6R/N1R proteins defines a novel, conservedDNA-binding domain (the KilA-N domain) that is found in a wide range ofproteins of large bacterial and eukaryotic DNA viruses. The KilA-N domainis suggested to be homologous to the fungal DNA-binding APSES domain. Weprovide evidence for the KilA-N and APSES domains sharing a common foldwith the nucleic acid-binding modules of the LAGLIDADG nucleases and theamino-terminal domains of the tRNA endonuclease. The amino-terminal moduleof the Bro proteins is another, distinct DNA-binding domain (the Bro-Ndomain) that is present in proteins whose domain architectures parallelthose of the KilA-N domain-containing proteins. A detailed analysis of theKilA-N and Bro-N domains and the associated domains points to extensivedomain shuffling and lineage-specific gene family expansion within DNAvirus genomes. CONCLUSIONS: We define a large class of novel viralDNA-binding proteins and their cellular homologs and identify their domainarchitectures. On the basis of phyletic pattern analysis we presentevidence for a probable viral origin of the fungus-specific cell-cycleregulatory transcription factors containing the APSES DNA-binding domain.We also demonstrate the extensive role of lineage-specific gene expansionand domain shuffling, within a limited set of approximately 24 domains, inthe generation of the diversity of virus-specific regulatory proteins.
