Figure 3.
Figure 3. Overall Shape and Domain Structure of AlkA(A and
B) Course of the AlkA polypeptide chain, with elements of
secondary structure assigned and colored accordingly (blue = β
sheet, red/orange = α helix, WHITE = nonrepetitive elements).
The arrow in (A) shows the location of the proposed enzyme
active site. The view in (B) is related to that in (A) by
rotation of vert,
similar 180°.(C) The AlkA protein consists of three domains:
an Image -terminal mixed α-β structure (Domain 1, blue); a
central seven-helix bundle (Domain 2, red; αD through αJ), and
a C-terminal domain of four α helices (Domain 3, yellow; αC
and αK through αM). A paucity of intersubunit contacts allows
some movement of domain 3 with respect to the rest of the
protein. The conserved helix-hairpin-helix motif, consisting of
helices αI and αJ and the intervening β turn, is located on
one side of this interdomain cleft.(D) The solvent-accessible
surface of AlkA, colored according to electrostatic potential
(blue, positively charged; red, negatively charged), reveals a
cleft at the junction of domains 2 and 3, which is unusually
rich in aromatic residues. Jutting into the cleft is the
catalytically essential residue Asp-238. The neighboring Asp
residue at position 237, which lies at the periphery of the
aromatic cleft, is not essential for glycosylase activity. A
number of lysines and arginines (blue), which could potentially
interact with DNA backbone phosphates, decorate the protein
surface around the aromatic cleft. This figure was created using
the program GRASP ([33]).
The above figure is reprinted
by permission from Cell Press:
Cell
(1996,
86,
321-329)
copyright 1996.
vert,
similar 180°.(C) The AlkA protein consists of three domains:
an Image -terminal mixed α-β structure (Domain 1, blue); a
central seven-helix bundle (Domain 2, red; αD through αJ), and
a C-terminal domain of four α helices (Domain 3, yellow; αC
and αK through αM). A paucity of intersubunit contacts allows
some movement of domain 3 with respect to the rest of the
protein. The conserved helix-hairpin-helix motif, consisting of
helices αI and αJ and the intervening β turn, is located on
one side of this interdomain cleft.(D) The solvent-accessible
surface of AlkA, colored according to electrostatic potential
(blue, positively charged; red, negatively charged), reveals a
cleft at the junction of domains 2 and 3, which is unusually
rich in aromatic residues. Jutting into the cleft is the
catalytically essential residue Asp-238. The neighboring Asp
residue at position 237, which lies at the periphery of the
aromatic cleft, is not essential for glycosylase activity. A
number of lysines and arginines (blue), which could potentially
interact with DNA backbone phosphates, decorate the protein
surface around the aromatic cleft. This figure was created using
the program GRASP ([33]).