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Figure 1.
Fig. 1. Structural plasticity of CK2α in the ATP binding
region. (a) Main-chain RMSDs after global 3D fit. Black curve:
hsCK2α^1–335/emodin complex fitted on
hsCK2α^1–335/AMPPNP/sulfate (PDB file: 2PVR);^23 red curve:
hsCK2α^1–335/emodin complex fitted on zmCK2α/emodin (PDB
file: 1F0Q^11). The conformational deviations at the ATP-binding
loop and at the hinge region are discussed in the text while
those at the β4–β5 loop (part of the interface to CK2β) and
the so-called CMGC insert (protein docking module typical for
all CMGC kinases) are not important in the context of this
study. The RMSDs were minimized with a least-squares algorithm
implemented in BRAGI.^24 (b) Pairwise structural comparisons of
the hinge regions of various maize and human CK2α
structures specified by their PDB codes. The given values are
minimized RMSDs (in angstroms) for all main-chain atoms from
Phe113 to Phe121 calculated with the program LSQKAB from the
CCP4 suite.^19 Two conformational clusters are indicated by a
colored background. (c) Stereo picture to illustrate the
structural adaptations of hsCK2α^1–335 upon ligand binding.
The picture shows the hsCK2α^1–335/emodin structure of this
study (yellow carbon atoms) and—after structural
superimposition—the hsCK2α^1–335/AMPPNP/sulfate complex of
PDB file 2PVR^23 (black carbon atoms). The drawn parts of the
hsCK2α^1–335/emodin structure are covered with electron
density (contour level of 1 σ) in different colors (green for
the enzyme, blue for emodin, and red for water). The electron
density around Glu114 is weaker because this side chain occurs
in two alternate conformations (only one conformation is shown).
The figure was drawn with BobScript^25 and Raster3D.^26 (d)
Stereo picture to demonstrate the major structural differences
between the emodin complexes of hsCK2α^1–335 (yellow carbon
atoms and backbone traces) and zmCK2α (PDB file 1F0Q;^11 gray
carbon atoms and backbone traces). The division of the hinge
region into two conformational clusters, which is apparent from
(b), is illustrated by the backbone traces of the seven
structures included in the computational analysis. Two pieces of
the final electron density are drawn with a contour level of 1
σ. The purple dotted line indicates a hydrogen bond between
His160 and Arg47 across the ATP-binding cleft of zmCK2α.
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