Three protein kinase structures define a common motif Susan Serota Taylor, Elzbieta Radzio-Andzelm  Structure  Volume 2, Issue 5, Pages 345-355 (May 1994) DOI: 10.1016/S0969-2126(00)00036-8

Figure 1 Ribbon diagrams comparing (a) MAPK, (b) PKA and (c) Cdk2 viewed with the small lobe towards the top. In each structure the amino-terminal segment is shown in purple and the remainder in pink. Peptide insertions are shown in yellow. The inhibitor peptide co-crystallized with the C-subunit of PKA is shown in red. MgATP is shown in green with the magnesium ions indicated as crosses. The conserved buried ion pair corresponding to Arg280 and Glu208 in PKA is shown in each structure with the side chains in yellow. In MAPK (a), the side chains of Arg146, Arg170, Arg65 and Arg68, which are potential ligands for the phosphate, are indicated in yellow with the side chains of the phosphorylation sites, Tyr185 and Thr183 in white. Also shown in yellow is the ion pair Arg299 and Glu195. In the C-subunit of PKA (b), the side chains of Arg165, Lys189 and His87 are shown in yellow and phosphorylated Thr197 is shown in white. The position of the single amino acid insert in the linker region of PKA, Gly125, is also indicated in yellow. The detergent molecule that occupies the myristylation site is shown as a yellow CPK structure on the left. In Cdk2 (c), the side chains of the two phosphorylation sites are shown with Thr160 in white and Tyr15 in yellow. Also shown in yellow are Arg150 and Arg126, potential ligands for the phosphate, and the buried ion pair, Arg274 and Glu172. Structure 1994 2, 345-355DOI: (10.1016/S0969-2126(00)00036-8)

Figure 1 Ribbon diagrams comparing (a) MAPK, (b) PKA and (c) Cdk2 viewed with the small lobe towards the top. In each structure the amino-terminal segment is shown in purple and the remainder in pink. Peptide insertions are shown in yellow. The inhibitor peptide co-crystallized with the C-subunit of PKA is shown in red. MgATP is shown in green with the magnesium ions indicated as crosses. The conserved buried ion pair corresponding to Arg280 and Glu208 in PKA is shown in each structure with the side chains in yellow. In MAPK (a), the side chains of Arg146, Arg170, Arg65 and Arg68, which are potential ligands for the phosphate, are indicated in yellow with the side chains of the phosphorylation sites, Tyr185 and Thr183 in white. Also shown in yellow is the ion pair Arg299 and Glu195. In the C-subunit of PKA (b), the side chains of Arg165, Lys189 and His87 are shown in yellow and phosphorylated Thr197 is shown in white. The position of the single amino acid insert in the linker region of PKA, Gly125, is also indicated in yellow. The detergent molecule that occupies the myristylation site is shown as a yellow CPK structure on the left. In Cdk2 (c), the side chains of the two phosphorylation sites are shown with Thr160 in white and Tyr15 in yellow. Also shown in yellow are Arg150 and Arg126, potential ligands for the phosphate, and the buried ion pair, Arg274 and Glu172. Structure 1994 2, 345-355DOI: (10.1016/S0969-2126(00)00036-8)

Figure 1 Ribbon diagrams comparing (a) MAPK, (b) PKA and (c) Cdk2 viewed with the small lobe towards the top. In each structure the amino-terminal segment is shown in purple and the remainder in pink. Peptide insertions are shown in yellow. The inhibitor peptide co-crystallized with the C-subunit of PKA is shown in red. MgATP is shown in green with the magnesium ions indicated as crosses. The conserved buried ion pair corresponding to Arg280 and Glu208 in PKA is shown in each structure with the side chains in yellow. In MAPK (a), the side chains of Arg146, Arg170, Arg65 and Arg68, which are potential ligands for the phosphate, are indicated in yellow with the side chains of the phosphorylation sites, Tyr185 and Thr183 in white. Also shown in yellow is the ion pair Arg299 and Glu195. In the C-subunit of PKA (b), the side chains of Arg165, Lys189 and His87 are shown in yellow and phosphorylated Thr197 is shown in white. The position of the single amino acid insert in the linker region of PKA, Gly125, is also indicated in yellow. The detergent molecule that occupies the myristylation site is shown as a yellow CPK structure on the left. In Cdk2 (c), the side chains of the two phosphorylation sites are shown with Thr160 in white and Tyr15 in yellow. Also shown in yellow are Arg150 and Arg126, potential ligands for the phosphate, and the buried ion pair, Arg274 and Glu172. Structure 1994 2, 345-355DOI: (10.1016/S0969-2126(00)00036-8)

Figure 2 Sequence alignment of PKA, MAPK and Cdk2. The sequences are aligned and correlated with the elements of secondary structure in each kinase. The β -strands that align in all three structures are colored blue; the non-conserved strand, β 9, is shown in green. The α -helices that superimpose (D, E, F and H) are in pink, conserved but displaced helices are in light pink, and non-conserved helices are in purple. Ligands or potential ligands to the phosphorylation site (Cdk2, PKA and MAPK) are indicated by blue triangles. Phosphorylation sites in the activation loops are indicated by arrows. Highly conserved residues are indicated by red dots. The conserved regions (I–XI) defined by Hanks et al.[1] are also indicated. Functional loops are labeled and shown in yellow. Structure 1994 2, 345-355DOI: (10.1016/S0969-2126(00)00036-8)

Figure 3 Ribbon diagram of the catalytic subunit of PKA highlighting the regions that are variable and conserved in Cdk2 and MAPK. Only the core of the C-subunit (residues 40–300) is shown. Conserved β -strands that superimpose (1 to 8) are shown in blue while the variable β -strand 9 is shown in pale green. Conserved α -helices that superimpose (D, E, F and H) are shown in pink, while conserved but displaced α -helices (C, G and I) are shown in red, and the non-conserved α -helix B is in purple. Conserved residues are shown as black dots. ATP and the side chains of Asp166, Asp184, Arg280 and Glu208 are shown in black. The magnesium ion binding the β - and γ -phosphates is shown as a black dot. Phosphorylated Thr197 is indicated by the yellow arrow. Functional loops are labeled and shown in yellow. The protein kinase inhibitor peptide PKI (5–24) is also shown. Structure 1994 2, 345-355DOI: (10.1016/S0969-2126(00)00036-8)

Figure 4 Stereoview showing the superimposition of the α - carbon backbones of PKA, Cdk2 and MAPK. (a) Superimposition of PKA (turquoise) and MAPK (pink). (b) All three structures are superimposed, with PKA in blue, Cdk2 in orange and MAPK in red. (c) Superimposition of PKA (turquoise) and Cdk2 (pink). The phosphorylation sites are indicated as CPK structures (Thr197 of PKA in yellow; Thr160 of Cdk2 in pink; Tyr15 of Cdk2 in green; Thr183 and Tyr185 of MAPK in pink). ATP and the inhibitor peptide, PKI (5–24) are shown in yellow for PKA. N and C indicate the amino and carboxyl termini, respectively. Structure 1994 2, 345-355DOI: (10.1016/S0969-2126(00)00036-8)

Figure 4 Stereoview showing the superimposition of the α - carbon backbones of PKA, Cdk2 and MAPK. (a) Superimposition of PKA (turquoise) and MAPK (pink). (b) All three structures are superimposed, with PKA in blue, Cdk2 in orange and MAPK in red. (c) Superimposition of PKA (turquoise) and Cdk2 (pink). The phosphorylation sites are indicated as CPK structures (Thr197 of PKA in yellow; Thr160 of Cdk2 in pink; Tyr15 of Cdk2 in green; Thr183 and Tyr185 of MAPK in pink). ATP and the inhibitor peptide, PKI (5–24) are shown in yellow for PKA. N and C indicate the amino and carboxyl termini, respectively. Structure 1994 2, 345-355DOI: (10.1016/S0969-2126(00)00036-8)

Figure 4 Stereoview showing the superimposition of the α - carbon backbones of PKA, Cdk2 and MAPK. (a) Superimposition of PKA (turquoise) and MAPK (pink). (b) All three structures are superimposed, with PKA in blue, Cdk2 in orange and MAPK in red. (c) Superimposition of PKA (turquoise) and Cdk2 (pink). The phosphorylation sites are indicated as CPK structures (Thr197 of PKA in yellow; Thr160 of Cdk2 in pink; Tyr15 of Cdk2 in green; Thr183 and Tyr185 of MAPK in pink). ATP and the inhibitor peptide, PKI (5–24) are shown in yellow for PKA. N and C indicate the amino and carboxyl termini, respectively. Structure 1994 2, 345-355DOI: (10.1016/S0969-2126(00)00036-8)

Figure 5 Superimposition of the α -carbon backbones for the small lobes of PKA (turquoise), Cdk2 (red) and MAPK (pink). The side chains of the conserved residues in the small lobe corresponding to Lys72 and Glu91 in PKA are indicated in green. The corresponding side chains in Cdk2, Lys33 and Glu51, are shown in yellow and in MAPK, Lys52 and Glu69 are shown in white. The ATP in PKA is shown in yellow. In all structures the α -carbon of the three glycines in the phosphate-anchoring loop (Gly50, Gly52 and Gly55 in PKA, Gly11, Gly13, and Gly16 in Cdk2, and Gly30, Gly32 and Gly35 in MAPK) are shown in space-filling representation. Structure 1994 2, 345-355DOI: (10.1016/S0969-2126(00)00036-8)

Figure 6 Comparison of the activation loops in (a) MAPK, (b) PKA and (c) Cdk2. Three loops are shown: the glycine-rich, phosphate-anchoring loop between β -strands 1 and 2; the activation loop following β 9, and the P+1 loop between the phosphorylation site and the conserved glutamate. Also shown are the C-helix and β 9. The α -carbons of the glycines in the β 1–β 2 loop as well as the phosphorylation sites are shown as CPK structures. In (a), potential side chains that could ligate the phosphates (Arg65, Arg68, Arg146 and Arg170) are highlighted in red while conserved residues (Lys52, Glu69, Glu195 and Arg299) are shown in yellow. In PKA (b), the side chains of ligands to phosphothreonine are highlighted in red (Lys189, Arg165 and His87); conserved residues (Lys72, Glu91, Arg280 and Glu208) as well as Thr197 are shown in yellow. In Cdk2 (c), residues that may come close to the phosphorylated Thr160, (Thr47, Arg50, Arg126 and Arg150) are highlighted in red; conserved residues (Lys33, Glu51, Glu172 and Arg274) are shown in yellow. Structure 1994 2, 345-355DOI: (10.1016/S0969-2126(00)00036-8)

Figure 6 Comparison of the activation loops in (a) MAPK, (b) PKA and (c) Cdk2. Three loops are shown: the glycine-rich, phosphate-anchoring loop between β -strands 1 and 2; the activation loop following β 9, and the P+1 loop between the phosphorylation site and the conserved glutamate. Also shown are the C-helix and β 9. The α -carbons of the glycines in the β 1–β 2 loop as well as the phosphorylation sites are shown as CPK structures. In (a), potential side chains that could ligate the phosphates (Arg65, Arg68, Arg146 and Arg170) are highlighted in red while conserved residues (Lys52, Glu69, Glu195 and Arg299) are shown in yellow. In PKA (b), the side chains of ligands to phosphothreonine are highlighted in red (Lys189, Arg165 and His87); conserved residues (Lys72, Glu91, Arg280 and Glu208) as well as Thr197 are shown in yellow. In Cdk2 (c), residues that may come close to the phosphorylated Thr160, (Thr47, Arg50, Arg126 and Arg150) are highlighted in red; conserved residues (Lys33, Glu51, Glu172 and Arg274) are shown in yellow. Structure 1994 2, 345-355DOI: (10.1016/S0969-2126(00)00036-8)

Figure 6 Comparison of the activation loops in (a) MAPK, (b) PKA and (c) Cdk2. Three loops are shown: the glycine-rich, phosphate-anchoring loop between β -strands 1 and 2; the activation loop following β 9, and the P+1 loop between the phosphorylation site and the conserved glutamate. Also shown are the C-helix and β 9. The α -carbons of the glycines in the β 1–β 2 loop as well as the phosphorylation sites are shown as CPK structures. In (a), potential side chains that could ligate the phosphates (Arg65, Arg68, Arg146 and Arg170) are highlighted in red while conserved residues (Lys52, Glu69, Glu195 and Arg299) are shown in yellow. In PKA (b), the side chains of ligands to phosphothreonine are highlighted in red (Lys189, Arg165 and His87); conserved residues (Lys72, Glu91, Arg280 and Glu208) as well as Thr197 are shown in yellow. In Cdk2 (c), residues that may come close to the phosphorylated Thr160, (Thr47, Arg50, Arg126 and Arg150) are highlighted in red; conserved residues (Lys33, Glu51, Glu172 and Arg274) are shown in yellow. Structure 1994 2, 345-355DOI: (10.1016/S0969-2126(00)00036-8)

Figure 7 Comparison of the non-core regions of PKA, MAPK and Cdk2. PKA (ternary complex) is shown in turquoise with the extended segment, including the amino-terminal myristate (yellow) seen in the mammalian binary complex, shown in green. The carboxyl terminus of PKA is indicated as C(A). The carboxy-terminal segment of MAPK (residues 310–358) is shown in pink with the position of the carboxy-terminal residue Ser358 indicated as C(M). Cdk2 (residues 285–298) is in red with the carboxy-terminal residue, Leu298, indicated as C(C). Three conserved hydrophobic sites are indicated: site 1 (Trp296 in PKA, Phe285 in Cdk2, Tyr310 in MAPK) marks the end of the conserved catalytic core that is probably shared by all protein kinases; a second subsite, coincident with the carboxyl terminus of Cdk2, C(C), is shared by PKA and Cdk2 where the side chains of Phe318 (PKA) and Leu298 (Cdk2) converge. A third subsite is shared by PKA and MAPK and corresponds to the surface that is filled by Trp30 and Phe26 in PKA. Phe327 and Phe329 fill this site in MAPK. Structure 1994 2, 345-355DOI: (10.1016/S0969-2126(00)00036-8)