Difference between revisions of "Introduction to Kinases"
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===Substrate AAs and oddball kinases=== | ===Substrate AAs and oddball kinases=== | ||
Show structures of ser, thr and tyr | Show structures of ser, thr and tyr | ||
| − | + | ||
| + | ===Other kinds of kinases=== | ||
| + | <B>Histidine Kinases</B> phosphorylate themselves (autophosphorylate) on Histidine, before transferring that phosphate to an Aspartate on a substrate protein (so they are more correctly called Histidine-Aspartate Kinases). Histidine Kinases are common in bacteria (where they are part of the two-component signal transduction mechanisms), plants and lower eukaryotes, but are not found in animals. They are structurally distinct from serine/threonine/tyrosine kinases. Animals do have one class of kinases - mitochondrial pyuvate dehydrogenase kinases - which are structurally similar to histidine kinases, but phosphorylate on serine. | ||
| + | |||
| + | There is some evidence for phosphorylation of other amino acids, though these phoshoamino acids are very labile, making them difficult to work with, and the responsible kinases have not yet been found [add more detail, including histone phosphorylation]. | ||
| + | |||
| + | |||
| + | |||
===Special role of phosphotyrosine=== | ===Special role of phosphotyrosine=== | ||
| Line 22: | Line 29: | ||
==Biological Functions== | ==Biological Functions== | ||
| − | + | Protein Kinases modify virtually all regulated biochemical pathways and complex behaviors. A few of the more common and more universal roles of protein kinases include: | |
| − | Cell | + | |
| − | + | * Cell cycle control: cyclin dependent kinases (CDKs) control the various checkpoints that control cell cycle. | |
| − | DNA damage | + | * Response to extracellular stimuli: Receptor Kinases receive extracellular signals, and intracellular kinase cascades, such as the MAPK cascade, transduce this signal to various cellular components, including transcription. |
| − | + | * DNA damage response: The PIKK family are key mediators that perceive damaged DNA and co-ordinate the repair response. | |
| + | * Metabolic control | ||
| + | |||
==Kinases and Disease== | ==Kinases and Disease== | ||
| − | As key regulators, protein kinases have strong effects when misregulated. | + | As key regulators, protein kinases have strong effects when misregulated. Over 150 of the 518 human kinases are known to be mutated or misregulated in various diseases, while on the flip side, inhibition of kinases by drugs is a major area of research for disease therapy. Several small molecule drugs and antibodies targetting kinases (mostly receptor tyrosine kinases) are already on the market, mostly as anti-cancer targets, and hundreds of kinase inhibitors are in various stages of development |
A list of kinases implicated in disease, and some drug information is available at http://www.cellsignal.com/reference/kinase_disease.asp | A list of kinases implicated in disease, and some drug information is available at http://www.cellsignal.com/reference/kinase_disease.asp | ||
| − | |||
==Evolution, genomics== | ==Evolution, genomics== | ||
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| − | == | + | ==Accessory subunits and pathway data== |
| + | |||
| + | |||
| + | |||
| + | |||
==Structure and mechanism (enzymology revisited)== | ==Structure and mechanism (enzymology revisited)== | ||
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===Enz. mechanism=== | ===Enz. mechanism=== | ||
===Key residues and key group-specific residues=== | ===Key residues and key group-specific residues=== | ||
| + | |||
===Activation and control mechanisms=== | ===Activation and control mechanisms=== | ||
| − | + | Most kinases are themselves controlled by phosphorylation, either by other kinases or by other copies of themselves (autophosphorylation). This allows for complex control of a pathway by means of multiple interacting kinases. The most common form of regulation, found in most kinases, is 'activation loop phosphorylation': these kinases are normally inactive or weakly active, but when a residue on the activation loop, close to the catalytic center, is phosphorylated, the negative phosphate charge neutralizes an inhibitory positive charge in the HRD motif, increasing kinase activity. Other phosphorylation events can inhibit kinase activity, alter its interaction with other proteins, or change its subcellular localization. | |
| + | |||
| + | ====Regulatory Subunits==== | ||
| + | Several kinds of kinases have closely-associated proteins that regulate kinase activity. The best known are the cyclins, which act as regulators of the cell cycle CDK (Cyclin Dependent Kinase) kinases. [add detail]. Another is protein kinase A [more detail]. Other kinases are modulated by small molecules: PKC (Protein Kinase C) by ??, Protein Kinase A by cAMP... ... ... | ||
| + | |||
| + | ====Transactivation==== | ||
| + | Receptor kinases usually form dimers: both subunits can bind the extracellular ligand, and this binding alters the conformation of their intracellular kinase units. Transphosphorylation by each kinase of it's pair fully activates the kinase activity of the receptor. | ||
Revision as of 00:49, 29 December 2006
Contents
Introduction to Protein Kinases
Protein Kinases are enzymes that modify the function of other proteins by attaching phosphate groups to them. They are key controllers of most biochemical pathways and important in health and disease.
The kinase reaction
Protein Kinases bind substrate proteins and ATP and transfer a phosphate group from ATP to amino acids with free hydroxyl gropus (serine, threonine or tyrosine). Most kinases act on serine or threonine, while some are specific to tyrosine, and some act on all three. The phosphate group (PO4-) is negatively charged and changes the substrate protein in different ways – altering activity (including other kinases), the location of the protein, it’s turnover or it’s interactions with other proteins. These changes can be reversed by a separate class of enzymes called phosphatases, that remove the phosphate groups (graphic of kinase/phosphatase reaction).
Enzymology
Basic Reaction
Substrate AAs and oddball kinases
Show structures of ser, thr and tyr
Other kinds of kinases
Histidine Kinases phosphorylate themselves (autophosphorylate) on Histidine, before transferring that phosphate to an Aspartate on a substrate protein (so they are more correctly called Histidine-Aspartate Kinases). Histidine Kinases are common in bacteria (where they are part of the two-component signal transduction mechanisms), plants and lower eukaryotes, but are not found in animals. They are structurally distinct from serine/threonine/tyrosine kinases. Animals do have one class of kinases - mitochondrial pyuvate dehydrogenase kinases - which are structurally similar to histidine kinases, but phosphorylate on serine.
There is some evidence for phosphorylation of other amino acids, though these phoshoamino acids are very labile, making them difficult to work with, and the responsible kinases have not yet been found [add more detail, including histone phosphorylation].
Special role of phosphotyrosine
Tyrosine phosphoryation has been of particular interest to many biologists, due to its biological roles. Even though only x% of cellular protein is tyrosine phosphorylated (compared with y% on Ser, z% on thr), these sites have strong biological functions, particularly in terms of communication between cells. Most tyrosine phosphorylation is carried out by a distinct group of ePK kinases, called TK (tyrosine kinase), though several ser/thr-looking kinases also have tyrosine kinase abilities (so-called dual-specificity kinases). Most TKs are either receptor tyrosine kinases (RTKs) whose extracellular region senses extracellular signals, or are receptor-associated kinases (is this a term?) that are located near the surface of the cell and interact with RTKs.
Range of Biochemical Substrates
What does phosphorylation do? – activate, relocate etc.
Biological Functions
Protein Kinases modify virtually all regulated biochemical pathways and complex behaviors. A few of the more common and more universal roles of protein kinases include:
- Cell cycle control: cyclin dependent kinases (CDKs) control the various checkpoints that control cell cycle.
- Response to extracellular stimuli: Receptor Kinases receive extracellular signals, and intracellular kinase cascades, such as the MAPK cascade, transduce this signal to various cellular components, including transcription.
- DNA damage response: The PIKK family are key mediators that perceive damaged DNA and co-ordinate the repair response.
- Metabolic control
Kinases and Disease
As key regulators, protein kinases have strong effects when misregulated. Over 150 of the 518 human kinases are known to be mutated or misregulated in various diseases, while on the flip side, inhibition of kinases by drugs is a major area of research for disease therapy. Several small molecule drugs and antibodies targetting kinases (mostly receptor tyrosine kinases) are already on the market, mostly as anti-cancer targets, and hundreds of kinase inhibitors are in various stages of development
A list of kinases implicated in disease, and some drug information is available at http://www.cellsignal.com/reference/kinase_disease.asp
Evolution, genomics
Most human protein kinases share a common structural domain, the ePK (eukaryotic protein kinase) domain. Kinases with this domain are almost exclusively eukaryotic, and consitute one of the largest eukaryotic gene families, representing 1-4% of all genes in sequenced genomes. Comparison of the kinomes of several divergent genomes indicates that the most primitive eukaryote had about 35 distinct kinase functions. Humans have 518 protein kinase genes
Classification
Accessory subunits and pathway data
Structure and mechanism (enzymology revisited)
- in-depth analysis of the 3D structure, including secondary structure elements, key residues, faces for regulation, autophosphorylation, differences between groups etc.
Enz. mechanism
Key residues and key group-specific residues
Activation and control mechanisms
Most kinases are themselves controlled by phosphorylation, either by other kinases or by other copies of themselves (autophosphorylation). This allows for complex control of a pathway by means of multiple interacting kinases. The most common form of regulation, found in most kinases, is 'activation loop phosphorylation': these kinases are normally inactive or weakly active, but when a residue on the activation loop, close to the catalytic center, is phosphorylated, the negative phosphate charge neutralizes an inhibitory positive charge in the HRD motif, increasing kinase activity. Other phosphorylation events can inhibit kinase activity, alter its interaction with other proteins, or change its subcellular localization.
Regulatory Subunits
Several kinds of kinases have closely-associated proteins that regulate kinase activity. The best known are the cyclins, which act as regulators of the cell cycle CDK (Cyclin Dependent Kinase) kinases. [add detail]. Another is protein kinase A [more detail]. Other kinases are modulated by small molecules: PKC (Protein Kinase C) by ??, Protein Kinase A by cAMP... ... ...
Transactivation
Receptor kinases usually form dimers: both subunits can bind the extracellular ligand, and this binding alters the conformation of their intracellular kinase units. Transphosphorylation by each kinase of it's pair fully activates the kinase activity of the receptor.
