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Gly193 and Tyr194, Lys188 and Gly189 form two short antiparallel β strands separated by a turn of
three residues (Gly190, Ile191, and Gly192) not involved in main chain hydrogen bonds. The first
residue of the last helix, (helix F), which runs until Asp212, is Ser194.
Three Conserved Acidic Residues at the Enzyme Active Site
Page 95
There are four amino acids in the core domain sequence that are absolutely conserved among retroviral
integrases: Asp64, Asp116, Glu152, and Lys159. The three acidic residues form the conserved D,D-35-
E motif and have been shown to be essential for catalysis (see Section III.A). The role of Lys159 in
retroviral integrases is not obvious; its replacement with Val does not abolish catalytic activity, although
there is a decrease in strand transfer activity [20].
The first essential acidic residue, Asp64, is located in the middle of the first β strand, while Asp116 is in
a loop region right after the fourth β strand. These two residues define the active-site area and they are
right next to each other three-dimensionally with their α-carbons separated by only 6.7 Å. The closest
approach is 3.4 Å between Oδ1 of Asp64 and Cβ of Asp116. These residues are on the surface of the
molecule, not part of any obvious substrate-binding cleft. The third catalytically essential acidic residue,
Glu152, is in the disordered and hence crystallographically invisible region between Gly140 and
Met154. Its location therefore must be inferred from other parts of the structure and from available threedimensional
structures of related proteins. The location of Met154, the residue only two positions
upstream from Glu152, is known because of interpretable electron density. The distance between the αcarbons
of Glu152 and Met154 cannot be larger than about 7.3 Å, which constrains Glu152 to the
neighborhood of the two other essential carboxylates, allowing it to contribute to the formation of a
divalent metal-binding site.
More recently, a crystal structure of the avian sarcoma virus (ASV) integrase core domain was solved
[36]. Within this domain, ASV integrase has 24% sequence identity to the HIV-1 integrase core and, as
expected, its three-dimensional structure is remarkably similar. The ASV integrase core in its native
form has much better solution properties than the HIV-1 integrase core, and did not require any point
mutations to render it crystallizable. Due to this fact and perhaps also due to its different crystal packing
interactions, the crystal lattice of the ASV integrase core domain is somewhat more ordered than that of
HIV-1. The two three-dimensional structures can be aligned quite well, using 74 α-carbons, with an rms
deviation of only 1.4 Å in these α-carbon positions. The most remarkable difference between the two
structures is that in the ASV structure the electron density is interpretable in all parts of the molecule.
This is not to say, however, that serious disorder is not present. For example, in one particular loop, the
temperature factors are above 70 Å 2 for the α carbons, indicating larger than 1 Å mean displacement
value for these atoms. The corresponding
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