 |
PDBsum entry 1vsk
|
|
|
|
References listed in PDB file
|
 |
|
Key reference
|
|
|
Title
|
|
Structural basis for inactivating mutations and ph-Dependent activity of avian sarcoma virus integrase.
|
|
|
Authors
|
|
J.Lubkowski,
F.Yang,
J.Alexandratos,
G.Merkel,
R.A.Katz,
K.Gravuer,
A.M.Skalka,
A.Wlodawer.
|
|
|
Ref.
|
|
J Biol Chem, 1998,
273,
32685-32689.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
Crystallographic studies of the catalytic core domain of avian sarcoma virus
integrase (ASV IN) have provided the most detailed picture so far of the active
site of this enzyme, which belongs to an important class of targets for
designing drugs against AIDS. Recently, crystals of an inactive D64N mutant were
obtained under conditions identical to those used for the native enzyme. Data
were collected at different pH values and in the presence of divalent cations.
Data were also collected at low pH for the crystals of the native ASV IN core
domain. In the structures of native ASV IN at pH 6.0 and below, as well as in
all structures of the D64N mutants, the side chain of the active site residue
Asx-64 (Asx denotes Asn or Asp) is rotated by approximately 150 degrees around
the Calpha---Cbeta bond, compared with the structures at higher pH. In the new
structures, this residue makes hydrogen bonds with the amide group of Asn-160,
and thus, the usual metal-binding site, consisting of Asp-64, Asp-121, and
Glu-157, is disrupted. Surprisingly, however, a single Zn2+ can still bind to
Asp-121 in the mutant, without restoration of the activity of the enzyme. These
structures have elucidated an unexpected mechanism of inactivation of the enzyme
by lowering the pH or by mutation, in which a protonated side chain of Asx-64
changes its orientation and interaction partner.
|
|
|
|
|
|
|
|
Figure 1.
Fig. 1. The active site of ASV IN (catalytic core
domain). A, F[o]  F[c]
difference density "omit" map, contoured at 2.5  , showing
the position of the side chain of D64N (blue) compared with the
side chain of Asp-64 (brown) in the active conformation. The
hydrogen bonding pattern of a structurally conserved water
molecule observed in all ASV IN structures is also shown. B,
hydrogen bonding of the side chain of D64N with Asn-160. The
hydrogen bonding pattern of a structurally conserved water
molecule observed in all ASV IN structures is also shown. C,
hydrogen bonding of the side chain of Asp-64 with the
structurally conserved water.
|
|
Figure 2.
Fig. 2. The active site of ASV IN (catalytic core domain)
with bound zinc cation(s). A, 2F[o] F[c]
density map, contoured at 2.5 , showing
the bound Zn2+ hydrogen bonded only to the side chain of
Asp-121. The side chain of D64N is hydrogen bonded to Asn-160.
B, a previously determined structure of ASV IN, showing the
bound zinc cations hydrogen bonded to the side chains of Asp-64
and Asp-121.
|
|
|
|
|
|
The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(1998,
273,
32685-32689)
copyright 1998.
|
|
|
|
|
|
|
