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grase and the MuA transposase extends until the carboxyl termini of their respective catalytic domains
with three very similarly positioned and oriented α helices.
Page 98
Limited three-dimensional alignment between the four molecules can be accomplished by identifying
structurally homologous stretches along the polypeptide chains if this search is restricted to between the
first well-ordered amino terminal residue and the end of the last β strand. For the core domain of HIV-1
integrase, this corresponds to the region between Ile60 and Gln137. Using the corresponding region in
the MuA transposase, the two structures can be aligned with an rms deviation of 1.7 Å over 69 α-carbon
positions. The main differences between these structures are two insertions in the transposase core: an
11-residue β-stranded extension replacing the turn between the first and the second strand in the HIV-1
integrase core, and a 15-residue extension before helix B with no secondary structure. Both of these
extensions interact with the downstream nonspecific DNA-binding domain of the transposase. For HIV-
1 RNase H, the alignment results in a rms deviation of 2.0 Å over 48 alignable α-carbon positions. The
position of helix A is significantly different in RNase H, as it shifts more than 5 Å toward the β sheet.
There is also an additional 2.5 turn helix following the fourth β strand and a 5-residue loop after this
helix. For RuvC the alignment yields an rms deviation of 2.0 Å over 50 alignable α-carbon positions. In
this case, the differences are mostly the result of longer secondary structure elements in RuvC. Of all the
molecules compared, the HIV-1 integrase core is the smallest, with the most compact design in the
region where these alignments were performed. For comparison, let us mention again that the
homologous ASV integrase core can be aligned with an rms deviation of 1.4 Å over 74 α-carbon
positions in this region.
Both topological similarity and three-dimensional homology with the MuA transposase was expected
based on the similarity of the reactions the enzymes catalyze, but the relationship with RNase H and
RuvC was a surprise. This discovery led to the proposal of a new polynucleotidyl transferase
superfamily. All the members of the superfamily are divalent metal ion-dependent endonucleases, and
they all leave 3'-OH and 5'-phosphate groups at the site of cleavage. All the members of the superfamily
display their catalytically essential acidic residues at the same general location. There are three such
residues in HIV-1 integrase, RNase H, and the MuA transposase, while there are four in RuvC. Two of
these residues are always located on the same three-dimensional structural elements, while the location
of the third varies. The Asp64 residue HIV-1 integrase corresponds to Asp443 in HIV-1 RNaseH, Asp7
in RuvC, and Asp269 in the MuA transposase. Based on the three-dimensionally aligned structures, the
α-carbon positions of these residues cluster quite well around that of HIV-1 integrase, with an rms
deviation of 0.84 Å. All these residues are located in the middle of first β strand. The side chain torsion
angle, Chi 1, is
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