Nucleic Acids Research, Vol 25, Issue 22 4626-4638, Copyright © 1997 by Oxford University Press
JZ Dalgaard, AJ Klar, MJ Moser, WR Holley, A Chatterjee and IS Mian
The LAGLIDADG and HNH families of site-specific DNA endonucleases encoded
by viruses, bacteriophages as well as archaeal, eucaryotic nuclear and
organellar genomes are characterized by the sequence motifs 'LAGLIDADG' and
'HNH', respectively. These endonucleases have been shown to occur in
different environments: LAGLIDADG endonucleases are found in inteins,
archaeal and group I introns and as free standing open reading frames
(ORFs); HNH endonucleases occur in group I and group II introns and as
ORFs. Here, statistical models (hidden Markov models, HMMs) that encompass
both the conserved motifs and more variable regions of these families have
been created and employed to characterize known and potential new family
members. A number of new, putative LAGLIDADG and HNH endonucleases have
been identified including an intein-encoded HNH sequence. Analysis of an
HMM-generated multiple alignment of 130 LAGLIDADG family members and the
three-dimensional structure of the I- Cre I endonuclease has enabled
definition of the core elements of the repeated domain (approximately 90
residues) that is present in this family of proteins. A conserved
negatively charged residue is proposed to be involved in catalysis.
Phylogenetic analysis of the two families indicates a lack of exchange of
endonucleases between different mobile elements (environments) and between
hosts from different phylogenetic kingdoms. However, there does appear to
have been considerable exchange of endonuclease domains amongst elements of
the same type. Such events are suggested to be important for the formation
of elements of new specficity.
ARTICLES
Statistical modeling and analysis of the LAGLIDADG family of site- specific endonucleases and identification of an intein that encodes a site-specific endonuclease of the HNH family
NCI-Frederick Cancer Research and Development Center, ABL-Basic Research Program, PO Box B, Building 549, Room 154, Frederick, MD 21702- 1202, USA. dalgaard@ncifcrf.gov
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