Cell News 2/2014
16
Research news
Substrate recognition by protein kinases is crucial for catalysis
and regulation in the cellular signaling
Yosr Z. Haffani
1, 2
1
LR Biotechnology and Valorisation of Bio-Geo Ressources LR11-ES31, University of Manouba, Institute of Biotechnology
of Sidi-Thabet. Technology Park of Sidi-Thabet. Tunisia; email:
2
Functional Architecture of the Cell, German Cancer Research Center (DKFZ). Im Neuenheimer Feld 280, 69120 Heidelberg,
Germany
Abstract
Eukaryotic protein kinases are members of a ¨super-family¨ of
enzymes that catalyze the addition of phosphate from adeno-
sine triphosphate (ATP) onto target hydroxyl groups in protein
substrates. This causes profound effects on the substrate such as
changing its activity or association with other proteins. Over 500
protein kinases in the human genome have protein phospho-
rylation activity and are perhaps one of the most common com-
ponents of signaling pathways, which are involved in different
biological functions. Key properties account for the prevalence
of many different biological functions. Protein kinases are able
to define proper switching and substrate recognition mecha-
nisms. Switching refers to the property, of these enzymes to stay
discretely at the activated state or in a resting state, and this is
very important for their ability to tightly regulate and control
signaling cascades. With a great number of protein kinases and
a multitude of protein substrates, which co-exist together, the
kinases ensure substrate recognition specificity by various me-
chanisms using as a primary determinant short peptide motifs.
In addition, these “primary” recognition mechanisms establish a
further level of specificity by secondary interactions.
Introduction
Signal transduction through protein kinases is a critical process
in both plant and animals. The sequencing of the human geno-
me revealed more than 500 members of this superfamily invol-
ved in cellular response like development, metabolism and cell
cycle progression (Manning et al., 2002). Kinases are proteins
with a catalytic domain that can transfer the gamma-phosphate
of adenosine triphosphate (ATP) to hydroxyl groups in target
protein interactors (Hanks and Hunter, 1995). The phospho-
recognition interaction is made by specific modules that lead
to conformational changes, affects proteins function and may
also trigger the formation of high order molecular assemblies.
The conserved nature of the ATP-active sites of protein kina-
ses in eukaryotes provides the same basic chemical reaction for
catalysis. In light of the multitude of protein substrates, many
of which can exist within the cell at the same time and at the
same place, the kinases face the problem to correctly target their
substrate through very specific catalytic switching and substra-
te recognition mechanisms that ensure targeting (Nolen et al.,
2004). Chemical and pharmacological efforts to discover small
molecule inhibitors for kinases have developed ATP-competitive
compounds (Hubbard, 2002). These approaches promote rapid,
Figure 1.
Protein kinases share a
conserved catalytic core. A. Ribbon
representation of a protein kinase
ATP substrate complex. Shown
is PKA kinase in complex with a
small peptide substrate and ATP
(PDB ID 2PHK). B. The conserved
core consists of a small N-lobe, a
large C-lobe, ATP and a pepti-
de binding pocket. Interactions
between the peptide substrate
and a region in the kinase called
the activation segment or A-loop
dictates the allowed or consensus
sequence for a particular kinase.
This level of recognition is often
augmented by additional targeting
sites. The N-lobe and C-lobe are
colored yellow and purple, respec-
tively. The ATP molecule is colored
brown and red. A substrate peptide
is colored light blue, containing
the phospho-acceptor residue.
