Figure 1.
The structure of protein kinase A (PKA).
PKA is shown in its active conformation with ATP in green sticks and Mn2+ as black spheres. β-strands, helices and loops are labeled as in Knighton et al. [45]. The active site is situated between the small and large lobes, located above and below ATP respectively. CL: catalytic loop; MPL: magnesium-positioning loop.
Table 1.
Active-conformation kinase structures.*
Figure 2.
The fifteen active-conformation kinase structures listed in Table 1 were aligned using our modified Procrustes approach. Shown in green sticks is the ATP or ATP analog molecule of each structure. Each kinase is colored uniquely.
Figure 3.
Each sphere represents a conserved residue. Red indicates full conservation of a particular amino acid in all fifteen kinase structures; orange, conservation in thirteen or fourteen structures; and yellow, conservation in eleven or twelve structures. Blue spheres indicate full conservation of an amino-acid category. The ATP molecule of protein kinase A is shown in green sticks. (A) The consensus structure consisting of the forty-four points listed in Table 2. (B) The consensus structure overlaid on the multiple alignment.
Table 2.
Conserved residues found in the active-conformation kinases listed in Table 1.
Figure 4.
The atypical kinases (A) Rio2 and (B) transient receptor potential channel kinase (ChaK).
Figure 5.
Residue variability in positioning the γ-phosphate of ATP.
In each kinase the catalytic aspartic acid is shown in red and the positively-charged residue that interacts with the γ-phosphate of ATP is shown in yellow with nitrogen atoms colored blue. ATP is shown in green sticks. (A) Protein kinase A, (B) activated CDC42 kinase 1, (C) channel kinase, and (D) Rio2 kinase.
Figure 6.
Variations in the catalytic lysine.
(A) In almost all protein kinases (such as protein kinase A shown) a lysine residue originating from β-strand 3 interacts with the α- and β-phosphates of ATP. This lysine is required for catalytic activity and has been termed the catalytic lysine. (B) In channel kinase (ChaK), the homologous lysine interacts with the α-phosphate and the adenine ring of ATP. An unique arginine residue located on β-strand 2 instead interacts with the α- and β-phosphates. (C) In protein kinase with no lysine 1 (WNK1, PDB code: 1T4H [22]), the catalytic lysine is present but originates from β-strand 2, much like the arginine from ChaK. ATP is shown in green sticks. Potential hydrogen bonds between the positively charged residues and ATP are shown as dashed lines, and nitrogen atoms are colored blue. The WNK structure has no ATP or ATP analog.
Figure 7.
Substrate-specific variability.
Cross-eyed stereo views of (A) protein kinase A and (B) Akt2. Bound substrate peptides are shown in red sticks. Atoms belonging to non-conserved residues within 10 Å of the substrate peptide are shown as colored spheres. Red: atoms within 2 Å of a conserved residue; orange: atoms between 2 and 4 Å of a conserved residue; yellow: atoms between 4 and 6 Å of a conserved residue; green: atoms between 6 and 8 Å of a conserved residue; cyan: atoms between 8 and 10 Å of a conserved residue; and blue: atoms more than 10 Å from a conserved residue.
Figure 8.
PDK1 was modeled using the consensus guided approach outlined in the Results and Methods sections. (A) The best model is in blue and the actual structure in red (PDB code: 1H1W). Structures are shown aligned based on Cα RMSD. (B) Residues 201–225, comprising the floor of the active site, are highlighted as aligned on side chains. (C) Residues from the non-conserved regions of the substrate binding groove (residues 166–175 and 278–305) are shown as aligned on side chains. ATP from the true structure of PDK1 is shown in green sticks.
Figure 9.
Modeling an atypical kinase, Rio2.
(A) The best model is in blue and the actual structure in red (PDB code: 1ZAO). Structures are shown aligned based on Cα RMSD. Residues 128–142 from the model are hidden because they are disordered in the actual structure. (B) Residues 214–237 are highlighted as aligned on side-chains. ATP is shown in green sticks.