Biology Reference
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Figure 1. The sequence alignment of the HATPase_c domain of VicK in S. pneumoniae and 2c2a.
The symbols below the alignment represent the similarity between two proteins. “*” denotes identical
residues between two sequences, “means similar residues, ”. means a bit different and blank means
completely different. Schematic alignment diagram was made by the program ClustalX.
A 3D Model of the VicK HATPase_c Domain of S. pneumoniae
Based on the X-ray diffraction crystal structure of the homologous domain of the
Thermotoga maritima , a 3D model for the VicK HATPase_c domain of S. pneumoniae
was constructed. Figure 2A shows the final structure of this model that was checked
and validated using structure analysis programs Prosa and Profile-3D [29]. This model
of 3D structure contains five stranded β-sheets and four α-helices, which form a two-
layered α/β sandwich structure. Figure 2B indicates that the model superposed well
with the homologous domain of Thermotoga maritima , with a root-mean-square de-
viation (RMSD) of the Cα atoms being about 1.34 Ǻ. The surface shape and general
electrostatic feature of the HATPase_c domain of VicK were shown in Figure 2C.
The ATP binding site consists of a relatively hydrophobic inner cavity and a larger
hydrophilic outer cavity. Both cavities are connected by a gorge-like channel, and are
consisted of highly conserved residues which can bind and fix the substrate. The inner
part lack of polar amino acid residues can accommodate the adenosine, while the outer
one rich in charged residues can bind the triphosphate.
Figure 2. The modeled structure of the VicK HATPase_c domain of S. pneumoniae . (A) The solid ribbon
representation of the structure model of the VicK HATPase_c domain. (B) Structure superposition of
sketch of modeled VicK structure with the template. (C) Shape and surface features of the ATP-
binding pocket of the VicK HATPase_c domain. The color denotes electrostatic potential of the
protein surface. The red and blue color show negative and positive charged potential respectively,
and the white surface means neutral potential of non-polar hydrophobic residues. The ATP-binding
pocket is divided into “inner” and “outer” parts. The loop covered on the pocket is shown as tube for
the sake of clearly demonstrating the hydrophobic inner part. The outer part of pocket is hydrophilic
because of many polar residues in the entrance of the pocket, including the polar loop structure. All
the pictures were generated by PyMol [http://www.pymol.org/].
 
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