Regulation of Protein Kinases Brad Nolen, Susan Taylor, Gourisankar Ghosh  Molecular Cell  Volume 15, Issue 5, Pages 661-675 (September 2004) DOI: 10.1016/j.molcel.2004.08.024

Figure 1 Defining the Activation Segment (A) The structure of CDK2 (1QMZ) showing the entire activation segment (yellow). (B) Nomenclature of the activation segment. The activation segment runs from the conserved DFG in the magnesium binding loop to the conserved APE in the P+1 loop and includes β9 and the activation loop. Though the αEF/αF loop is not part of the activation segment, it is discussed in the text so is labeled here. Molecular Cell 2004 15, 661-675DOI: (10.1016/j.molcel.2004.08.024)

Figure 2 Structure-Based Sequence Alignment of the Activation Segment of Active Protein Kinase Structures The secondary structure of the kinase core (based on the structure of PKA, 1ATP) is indicated above the alignment. Portions of the sequence that showed the greatest structural variability (RMSD > 2.0 Å2) in the superpositions are indicated by dashed lines in the secondary structure. Regions that consistently overlaid well are outlined in blue boxes. Primary phosphorylation sites observed in the active crystal structures are boxed in green and the residues that contact the primary phosphate in yellow. Secondary phosphorylation sites are boxed in cyan. Residues that interact with primary phosphorylation sites are boxed in yellow. Residues of the basic pocket of CMGC kinases are boxed in red. The hinge point at the beginning of the P+1 loop is indicated with a blue arrow. The anchor points of the activation segment are indicated by magenta boxes underneath the alignment. Amino acids in lowercase are disordered in the corresponding structures. Molecular Cell 2004 15, 661-675DOI: (10.1016/j.molcel.2004.08.024)

Figure 3 Activation Segment Superpostions (A) Overlay of active Ser/Thr kinases showing the position of the activation segment. Activation segments are colored according to the phylogenic group as defined in Manning et al. AGC, blue; CaMK, green; CMGC, cyan; CK1, yellow. The catalytic loop and helix αF are gray. The N-terminal anchor, as described in the text, consists of residues 184 to 190 (PKA numbering), while the C-terminal anchor includes residues 201 to 208. (B) Overlay of active tyrosine kinases showing position of the activation segment. Activation segments are colored as follows: IRK and IGF1K, blue; LCK, cyan; EGFRK, yellow; CSK, green and red (two conformations in crystal); c-KIT, pink. The catalytic loop and helix αF are gray. The N-terminal anchor, as described in the text, consists of residues 1150 to 1156 (IRK numbering), while the C-terminal anchor includes residues 1172 to 1179. Molecular Cell 2004 15, 661-675DOI: (10.1016/j.molcel.2004.08.024)

Figure 4 The N-Terminal Anchor of the Activation Segment The N-terminal anchor stretches from the magnesium-chelating aspartate to the end of β9 and is positioned at the back of the active site at the interface between the small (purple ribbons) and the large (blue-green ribbons) lobes. Three hydrogen bonds between β6 and β9 and characteristic of the active state and are often disrupted in the structures of inactive kinases, causing catalytically important residues such as E91 and D184 to become incorrectly positioned. A conserved hydrophobic residue in the magnesium binding loop (Phe185) mediates hydrophobic contacts with helix αC at the interface of the two lobes. The coordinates of 1ATP were used for this figure. Molecular Cell 2004 15, 661-675DOI: (10.1016/j.molcel.2004.08.024)

Figure 5 The C-Terminal Anchor (A) The C-terminal anchor of S/T kinases. The C-terminal anchor plays a critical role in positioning the substrate (yellow). The phosphorylated residue (Po) is positioned on a surface formed by the catalytic (green) and P+1 loops (cyan). The β and γ phosphates are shown for reference. The end of the activation segment is tacked down by the conserved glutamic acid from the APE motif, which interacts with a conserved arginine, forming a buried salt bridge. This figure was made using the coordinates for CDK2 with bound substrate peptide (1QMZ). Resides are identified using numbering from CDK2. (B) The C-terminal anchor of tyrosine kinases. Tyrosine kinases have a conserved proline at the beginning of the C-terminal anchor. The phosphorylatable phenol lays on top of this proline. Residues C-terminal to the tyrosine form a β sheet with the bulge in the P+1 and activation loops. The β and γ phosphates are shown for reference. The coordinates for the insulin-receptor kinase with bound substrate peptide were used for this figure (1IR3). Molecular Cell 2004 15, 661-675DOI: (10.1016/j.molcel.2004.08.024)

Figure 6 Comparison of the Activation Segment of Ser/Thr versus Tyr Kinases The large lobe of IRK (1IR3) was superimposed on Sky1p (1HOW; RMSD = 1.00 for 184 atoms) and the resulting rotation-translation matrix was used to superimpose each of the active TK structures (green) on the active S/T kinase structures (blue). For simplicity, some kinases, such as VEGFR (see text), were not included in this figure. Molecular Cell 2004 15, 661-675DOI: (10.1016/j.molcel.2004.08.024)

Figure 7 The Activation Loop Is Coupled to the αE/αF Loop Overlay of active and inactive structures of PKB (left), ERK2 (center), and CDK (right). Active structures are colored green and inactive are colored red. The following coordinate files were used: 1O6K, 1MRY; 1ERK, 2ERK; 1QMZ, 1HCK. Molecular Cell 2004 15, 661-675DOI: (10.1016/j.molcel.2004.08.024)

Figure 8 Crystal Packing and Alternate Conformations (A) Crystal packing disrupts the C-terminal anchor in DAPK. A large lobe overlay of the two molecules in the asymmetric unit of DAPK (1JKT) shows that the activation segment (green and red) adopts a different conformation in each molecule. The catalytic loop and regions C-terminal to the P+1 loop are colored gray. (B) Alternate conformations of the activation segment in a CK1 structure (1CKJ). (C) Flexibility in the activation loop of AGC kinases. Superpositions of PKA (1ATP, blue), PKB (1O6K, green), and PDK1 (1H1W, red) show differences in the torsion around Gly200 in PKA. Molecular Cell 2004 15, 661-675DOI: (10.1016/j.molcel.2004.08.024)

Figure 9 Differences in the RD Pocket of Ser/Thr and Tyrosine-Specific RD Kinases PKA (1ATP, yellow) and IRK (1IR3, green) typify the configuration of the RD pocket and the primary phosphorylation site for each class of kinase. Amino acids are labeled with PKA numbering except for pTyr1163, which is labeled in red. Molecular Cell 2004 15, 661-675DOI: (10.1016/j.molcel.2004.08.024)

Figure 10 Multiple Phosphorylation States and the Conformation of the Activation Segment of IRGF1RK The left panel shows the completely unphosphorylated segment (cyan) in comparison to the fully phosphorylated segment. The middle panel shows the doubly phosphorylated state, and the final panel shows the fully phosphorylated activation segment interacting with the substrate peptide. Asterisks mark phosphorylation sites. Parentheses around the asterisks indicates that the site is unphosphorylated. Blue asterisks indicate the primary phosphorylation site and black asterisks indicate secondary sites. The N- and C-terminal anchors are highlighted in yellow. Molecular Cell 2004 15, 661-675DOI: (10.1016/j.molcel.2004.08.024)

Figure 11 Overlay of Bruton's Tyrosine Kinase and the Activated Insulin Receptor Kinase The Cα trace of the activation loop of inactive BTK (1K2P, magenta) is overall very similar to the activation loop of active IRK (1IR3, cyan). The conserved arginine and aspartate residues in the catalytic loop, the phosphorylatable activation loop tyrosine, and the conserved aspartate in the magnesium binding loop are drawn as sticks. Molecular Cell 2004 15, 661-675DOI: (10.1016/j.molcel.2004.08.024)

Figure 12 A Phase Shift in the β6-β9 Sheet in the N-Terminal Anchor Inactivates Tie2 In the inactive structure (left panel, schematic based on 1FVR.PDB), the β6-β9 sheet is intact, but in the incorrect phase. In this conformation, Arg987 points away from the RD pocket and the magnesium binding loop is perturbed. Upon activation (right panel, predicted active conformation), Arg987 flips into the RD pocket, changing the phase of the β sheet and allowing the magnesium binding loop to adopt the active conformation. Molecular Cell 2004 15, 661-675DOI: (10.1016/j.molcel.2004.08.024)