2 The Kinase Active State
The tertiary structure and overall folding of the kinase catalytic domain is highly
conserved throughout the kinase family and harbours around 300 amino acids.
The first crystal structure of PKA in complex with ATP and a pseudosubstrate in
1991 paved the way for a better understanding of the catalytic mechanism, cofactor
binding and kinase regulation [15–17].
The canonical kinase catalytic domain fold consists of two domains, also called
lobes, which are connected to each other via a flexible hinge region. Both lobes
form a hydrophobic cleft which serves as binding site for ATP (Fig. 1a). The smaller
N-terminal lobe (N-lobe) comprises five β-sheets (β1–β5) and one helix called αC,
whereas the C-terminal lobe (C-lobe) is mainly alpha helical in structure (αD–αI).
Four main interactions were evident from the first PKA crystal structure [15–17]:
(1) The adenosine ring of ATP is placed in the catalytic centre and forms hydrogen
bonds with the hinge region amino acids. (2) A flexible loop region between
the sheets β1 and β2 harbours a glycine-rich sequence motif GXGXφG, where
φ refers to a hydrophobic residue which coordinates the ATP phosphates coining
the name phosphate-binding loop. (3) The β3-sheet contains a conserved VIAK
(Val-Ile-Ala-Lys) motif. The lysine adopts important structural features, by forming
a salt bridge with ATP phosphate groups and to a conserved glutamate residue
Fig. 1 Architecture of the kinase catalytic domain. (a) Conserved tertiary structure of a protein
kinase exemplified by CDK2 (PDB: 1QMZ). Catalytic active state of CDK2 in complex with ATP
and a peptide substrate. The P-loop is highlighted in pink, the αC-helix in blue, the hinge region in
yellow, the activation loop in green, ATP in orange and the peptide substrate in black. The Mg
2+ ion
is shown as green sphere. The N- and C-termini are marked. (b) Details of the ATP-binding site.
ATP and substrate are shown in stick representation. Colour schemes highlighting structural
elements are the same as in panel (a). Key hydrogen bonds are shown as dotted lines
Function, Structure and Topology of Protein Kinases
3
The tertiary structure and overall folding of the kinase catalytic domain is highly
conserved throughout the kinase family and harbours around 300 amino acids.
The first crystal structure of PKA in complex with ATP and a pseudosubstrate in
1991 paved the way for a better understanding of the catalytic mechanism, cofactor
binding and kinase regulation [15–17].
The canonical kinase catalytic domain fold consists of two domains, also called
lobes, which are connected to each other via a flexible hinge region. Both lobes
form a hydrophobic cleft which serves as binding site for ATP (Fig. 1a). The smaller
N-terminal lobe (N-lobe) comprises five β-sheets (β1–β5) and one helix called αC,
whereas the C-terminal lobe (C-lobe) is mainly alpha helical in structure (αD–αI).
Four main interactions were evident from the first PKA crystal structure [15–17]:
(1) The adenosine ring of ATP is placed in the catalytic centre and forms hydrogen
bonds with the hinge region amino acids. (2) A flexible loop region between
the sheets β1 and β2 harbours a glycine-rich sequence motif GXGXφG, where
φ refers to a hydrophobic residue which coordinates the ATP phosphates coining
the name phosphate-binding loop. (3) The β3-sheet contains a conserved VIAK
(Val-Ile-Ala-Lys) motif. The lysine adopts important structural features, by forming
a salt bridge with ATP phosphate groups and to a conserved glutamate residue
Fig. 1 Architecture of the kinase catalytic domain. (a) Conserved tertiary structure of a protein
kinase exemplified by CDK2 (PDB: 1QMZ). Catalytic active state of CDK2 in complex with ATP
and a peptide substrate. The P-loop is highlighted in pink, the αC-helix in blue, the hinge region in
yellow, the activation loop in green, ATP in orange and the peptide substrate in black. The Mg
2+ ion
is shown as green sphere. The N- and C-termini are marked. (b) Details of the ATP-binding site.
ATP and substrate are shown in stick representation. Colour schemes highlighting structural
elements are the same as in panel (a). Key hydrogen bonds are shown as dotted lines
Function, Structure and Topology of Protein Kinases
3