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Results and discussion Identification of the KilA-N domain in diverse viral proteins and its potential relationship to APSES and LAGLIDADG domains To determine the evolutionary affinities of the D6R/N1R amino-terminal regions, we initiated a PSI-BLAST search of the non-redundant (NR) protein database (National Center for Biotechnology Information), which was seeded with the sequence of the corresponding region from the variola virus D6R protein.
These hits precisely mapped to the APSES DNA-binding domain, which is shared by a range of fungus-specific transcription factors, such as MBP1p, SWI4p, PHD1p and SOK2p from Saccharomyces cerevisiae and Stunted A from Aspergillus nidulans [ 15].
For example, a search initiated with the KilA-N domain of Pseudomonas phage D3 Orf11 (gi:9635595) recovered the APSES domain of Saccharomyces MBP1p with an E-value of 0.
Reciprocal searches with the profiles of APSES domains, similarly recovered the KilA-N domain with borderline E-values.
As an example, a profile seeded with the MBP1p APSES domain and including all APSES domains in the NR database detects the N.
Given the availability of the three-dimensional structure of the APSES domain of the MBP1p protein [ 16, 17], we investigated this potential relationship using the KilA-N domain sequences for sequence-structure threading of the PDB database with the 3DPSSM, PSIPRED and combined-fold prediction algorithms.
8 for PSIPRED) that implied a 90% certainty of the KilA-N domain adopting the same fold as the APSES domain (PDB 1bm8/1bm1).
Threading with the combined-fold prediction algorithm also gave the MBP1p APSES domain as the best hit with a very high Z-score (Z = 60), suggesting that the KilA-N domain was highly likely to adopt the same fold as the APSES domain.
This predicted secondary structure of the KilA-N domain, with a head-to-tail dyad of a 2---strand-?
-helix unit (Figure 1a), is identical to the secondary structure seen in the conserved core of the APSES domains.
Structural comparisons using the DALI program [ 20], indicated that the core fold shared by the KilA-N and APSES domains is more distantly related to the LAGLIDADG site-specific DNA endonucleases and the amino-terminal domain of the tRNA splicing endonucleases (TEN domain) (Figure 1b) [ 21].
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