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Figure 1.
Figure 1. Overall Structure of DgkB and a Close-Up of the
Nucleotide-Binding Site
(A) Cartoon diagram of the DgkB
monomer in the asymmetric unit. α helices are gray, and β
strands and loops are green. ADP carbons and Mg1 (sphere) are
cyan. Secondary structure elements are labeled. Disordered
residues 145–157 are absent in the final model and are
indicated with a broken line. The predicted locations of the
insertions in human diacylglycerol kinases (see Figure 2) are
labeled IN1–3.
(B) Stereo cartoon of the YegS structure
(PDB code: 2BON, chain A) superimposed on DgkB. The orientations
of domains 1 and 2 differ slightly in the two structures, and,
to highlight their structural similarity, each domain of YegS
was superimposed independently onto the DgkB structure. DgkB is
colored as shown in (A), and YegS is tan. Disordered residues
are indicated with broken lines. Significant differences reside
in the predicted DgkB substrate-binding region (β8-α6 loop),
which is highlighted in bright green, and the corresponding YegS
region is brown.
(C) Stereo close-up view of the DgkB
nucleotide-binding site with omit electron density for ADP
contoured to 3σ. Bound waters are shown as red spheres.
Hydrogen bonds are indicated by broken lines.
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