Protein kinases :

cell signaling & implication in human

pathologies

20231120
The classical mitogen-activated protein
(MAP) kinase cascade is frequently
hyperactivated in lung and other cancers
owing to the overexpression or mutation
of receptor tyrosine kinases, such as the
epidermal growth factor receptor (EGFR),
ALK and MET, and more downstream
effectors that are most commonly RAS and
BRAF. Examples of drugs that target the
EGFR (gefitinib, erlotinib and osimertinib),
ALK (crizotinib, brigatinib and alectinib)
and MET (capmatinib and tepotinib) are
highlighted in red. The three approved
inhibitors of BRAF and the four approved
inhibitors of MEK1 and MEK2 are also
shown.
A schematic summary of the approved TKIs in 2001–2020. NMPA National Medical
Products Administration, MHLW Ministry of Health, Labor and Welfare, FDA Food and
Drug Administration Huang et al. J Hematol Oncol (2020) 13:143
Fig. 1: Timeline depicting important events in the
development and approval of kinase inhibitors
over the past 20 years since imatinib was
approved for treatment of CML in 2001.
Schematic
representation of
the physiological
roles and signaling
pathways of EGF
and VEGF and
their cognate
receptors and the
effect of antibodies
targeting these
signaling
molecules on CRC
progression and
metastasis. pY
means
phosphotyrosine
residues.

Biomedicines 2021, 9(1),

39; https://doi.org/10.3390/biomedicines9010039
FDA approved inhibitors and monoclonal antibodies
against Tyrosine kinase
 ibiology
• https://www.ibiology.org/biochemistry/protein-kinase/
• https://www.ibiology.org/biochemistry/protein-kinase/#part-1
• https://www.ibiology.org/biochemistry/protein-kinase/#part-2
• https://www.ibiology.org/biochemistry/protein-kinase/#part-3
• Protein Kinases: Structure, Function, and Regulation by Susan Taylor
• In this lecture, I have given an overview of protein kinase structure and function using cyclic AMP
dependent kinase (PKA) as a prototype for this enzyme superfamily. I have demonstrated what we
have learned from the overall structural kinome which allows us to compare many protein kinases
and also to appreciate how the highly regulated eukaryotic protein kinase has evolved. By
comparing many protein kinase structures, we are beginning to elucidate general rules of
architecture. In addition, I have attempted to illustrate how PKA is regulated by cAMP and how it is
localized to specific macromolecular complexes through scaffold proteins.
• Dr. Taylor received her BA in Chemistry from the University of Wisconsin-Madison and her PhD in
Physiological Chemistry from Johns Hopkins University. After completing a fellowship at the MRC
in Cambridge, she moved to the University of California, San Diego where she soon secured a
faculty position in the chemistry department. Shortly after joining UCSD, Taylor began working on
PKA and her lab has been investigating the mysteries of its structure and function ever since.
• Dr. Taylor has been a Howard Hughes Medical Institute Investigator since 1997. She is a member of
the National Academy of Sciences and the American Academy of Arts and Science and she has
been awarded numerous prizes for her groundbreaking research.
Questions
• Scientists have discovered a new drug that inhibits an overactive
kinase implicated in cancer. How do the scientists determine the
drug’s mechanism of action?
• To help you prepare for this, answer the following sub-questions:
• What are the key structural components of a kinase?
• How do kinases regulate signaling pathways inside the cell?
• Why is it important for the cell to have an on/off switch?
Protein Kinase
➢30% of all proteins may be modified

➢518 protein kinase genes=human kinome space

➢20% of all eukaryotic genes(human genome project)

➢Approx 30=tumor suppressor

➢218 genes=human diseases

➢Approx 100 dominant oncogenes

 Kinases Protein phosphorylation cell signaling

Reversible protein phosphorylation as a biological regulatory

mechanism
Edmond H. Fischer and Edwin G. Krebs
(1992 Nobel Prize for Physiology and Medicine).

Post-translational modification in the cell

• Cell growth/proliferation
• Differentiation
‘signal’ • Viability/survival
• Homeostasis
• Effector function (e.g. cytotoxicity, cytokine production)
• Cell death
Pathways leading to cancer
 Signal Transduction
and Kinase Pathways
Adaptor proteins

Nucleus Effector enzymes

MAP kinase,
• Transcription factors
– Bind consensus sequence on
promoter
– May form complexes
– May itself be transcribed
following cellular activation
 Major Classes of Cell-surface Receptors
About one dozen classes of
cell-surface receptors occur in
human cells. An overview of
signaling by the two receptor
systems that are covered in
this chapter (receptor tyrosine
kinases, RTKs, and TGF-ß
receptors.

The signal transduction

pathways used by RTKs.
 Classification

On the basis of amino acid :

❖ Tyrosine kinases, Receptor (EGFR,FGFR,PDGFR)

non receptor (JAK,src,Abl,MAPK)

❖ Serine threonine (PKC, Plk, Rho Kinases)

 Reactions and Types of Protein
Kinases

• Be able to recognize the three

amino acids with an –OH in
their R-group
• Serine
• Threonine
• Tyrosine
 General Structure of Kinases
1XKK: inactive • Bi-lobial structure
N-terminal lobe
2GS6: active
• N-termial lobe
• Mainly made of beta-sheets
and connecting loops
• One functionally important
helix
• Both lobes joined by a
loop called hinge.
C-terminal lobe • ATP binding pocket is in
the interface between the
lobes
• C-terminal lobe
• Mainly made of α-helices
• Activation loop spans both
N- and C-terminal lobes
18
 Important Structural Elements

…GxGxxG…

Helix-C

Hinge ATP
DFG……APE loop
• Glycine rich loop
• Closes in on the ATP

• Helix C
• Plays an important role in catalysis

• Hinge
• Adenosine moiety of the ATP makes
bidentate H-bond with this region

• Activation loop
• Starts with conserved sequence DFG and
ends with APE.

19
a) Dormant versus active protein-kinases. For clarity
reasons only a few molecular connections are shown
and one of the two Mg2+ atoms is omitted (situated
between β- and γ-phosphate). Note the rather
superficial binding of the substrate peptide in the
right panel. This explains, in part, why serine and
threonine are not good substrates; their hydroxyl
group does not get close enough to both the γ-
phosphate and the catalytic aspartate residue.
b) Active serine/threonine protein kinase (protein
kinase B). Note that the substrate-peptide penetrates
deeper into the cleft and that a short serine residue
easily reaches both ATP and the catalytic aspartate.
PDB files: 2GS6 and 2GS7
Highlighted residues in the catalytic domain of the EGFR (right
panel 3a): Gly695-Val702 (glycine-rich loop); Lys721 (in b3
sheet); Glu738 (in αC helix); Arg812 (in VHRDLA motif);
Asp813 (catalytic residue in VHRDLA motif); Asp831 (in DFG
motif); Leu833-Gly850 (activation segment); Val852-Met859
(P+1 substrate binding residues in spheres in the right panel of
figure 3a).
PDB file: 1O6K
Highlighted residues in the catalytic domain of protein kinase B
(PKB) (figure 3b): Gly159-Lys165 (glycine-rich loop); Lys181
(in β3 sheet); Glu200 (in αC Helix); Asp275 (in RDI motif);
Asp293 (in DFG motif); Leu296-Phe310 (activation segment);
Gly312-Glu320 (P+1 substrate binding residues in spheres in
figure 3b).