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Figure 4
Schematic domain structure of HIV-1 integrase as adapted from
Engelman et al. [19]. Structures of two domains, the catalytic core
extending from residues 50 to 212 [3] and the nonspecific
DNA-binding domain from residues 220 to 270 [28,29], have
recently been determined by x-ray crystallography and NMR
spectroscopy, respectively.
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the protease-resistant core of the protein [18,19]. Within this domain are three invariant residues that
comprise the “D,D-35-E motif” (see alignment in Figure 5). These are residues Asp64, Asp116, and
Glu152. Even conservative substitution of any of these residues leads to loss of all three in vitro
activities of integrase in parallel [19–21]. The D,D-35-E motif is also observed in retrotransposons and
some prokaryotic transposases. A truncated form of HIV-1 integrase consisting of residues 50 to 212 is
capable of disintegration [22], implying that the catalytic site is contained within this domain. These
observations and the absolute requirement for metals for in vitro activity have led to the proposal that
the three acidic residues constitute a divalent metal-binding site capable of binding one or two Mg 2+ or
Mn 2+ ions to form a catalytically active enzyme. As will be seen in later sections, the three-dimensional
structure of the core domain of HIV-1 integrase is consistent with this hypothesis. The catalytic
mechanism may be, therefore, similar to the one proposed by Beese and Steitz for the 3'–5' exonuclease
of E. coli DNA polymerase I [23]. It is proposed that for phosphate bond cleavage, one metal ion helps
form the attacking hydroxide ion while the other stabilizes a pentacovalent intermediate around the
phosphorus.
The C-terminus of HIV-1 integrase, consisting approximately of residues 210 to 288, includes the
dominant nonspecific DNA binding domain [24, 25], which has been more finely mapped to residues
220–270 [26]. The C-terminus is the least conserved region of retroviral integrases; only one residue,
Trp235, is absolutely invariant. However, it has been reported that removal of only five amino acids
from the C-terminus of HIV-1 integrase is enough to severely reduce its 3' processing and strand transfer
activities [27]. One notable feature of the C-terminus is its high proportion of positively charged
residues. As discussed in Section IV.E, the structure of part of this region has recently been determined
using NMR spectroscopic methods [28,29].
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