User:Alice Harmon/Sandbox 2: Difference between revisions
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Calcium-dependent protein kinases (CDPKs) are found in plants, green algae, and protists. In plants CDPKs are encoded by large gene families<ref> PMID:12805596</ref><ref>PMID:15695435</ref>, and they are involved in many cellular responses to stimuli such as hormones and environmental stress<ref>PMID: 24014579</ref>. In the apicomplexan protists ''Plasmodium falciparum'' (parasite that causes malaria) and ''Toxoplasma gondii'' (parasite that causes toxoplasmosis), CDPKs are encoded by small gene families, and they are involved in critical stages of the parasite life cycle <ref>PMID:23226109</ref><ref>PMID:20466936</ref>. | Calcium-dependent protein kinases (CDPKs) are found in plants, green algae, and protists. In plants CDPKs are encoded by large gene families<ref> PMID:12805596</ref><ref>PMID:15695435</ref>, and they are involved in many cellular responses to stimuli such as hormones and environmental stress<ref>PMID: 24014579</ref>. In the apicomplexan protists ''Plasmodium falciparum'' (parasite that causes malaria) and ''Toxoplasma gondii'' (parasite that causes toxoplasmosis), CDPKs are encoded by small gene families, and they are involved in critical stages of the parasite life cycle <ref>PMID:23226109</ref><ref>PMID:20466936</ref>. | ||
CDPKs are monomeric enzymes containing an amino-terminal protein kinase domain linked to a carboxy-terminal calcium-binding regulatory domain, which has sequence similarity to calmodulin, and they belong to the calmodulin-dependent protein kinase family<ref>PMID:1852075</ref>. CDPKs are regulated by the binding of | CDPKs are monomeric enzymes containing an amino-terminal protein kinase domain linked to a carboxy-terminal calcium-binding regulatory domain, which has sequence similarity to calmodulin, and they belong to the calmodulin-dependent protein kinase family<ref>PMID:1852075</ref>. CDPKs are regulated by the binding of Ca<sup>2+</sup> to the regulatory domain (called the calcium activation domain or CAD), which contains four EF-hand calcium-binding sites. CDPKs are thus are activated by processes that elevate the concentration of calcium inside cells. | ||
Crystal structures of inactive and active conformations of CDPK1 from ''Toxoplasma gondii'' show the dramatic conformation change that occurs upon the binding of calcium to the regulatory domain <ref> PMID:20436473 </ref>. See [[Eukaryotic Protein Kinase Catalytic Domain]] for a guide to their structure. | Crystal structures of inactive and active conformations of CDPK1 from ''Toxoplasma gondii'' show the dramatic conformation change that occurs upon the binding of calcium to the regulatory domain <ref> PMID:20436473 </ref>. See [[Eukaryotic Protein Kinase Catalytic Domain]] for a guide to their structure. | ||
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|'''Right scene''' - The crystal structure [[3hx4]] shows the '''active conformation''' of the kinase that is bound to calcium (green spheres) and the ATP analog ANP (also called AMPPNP; shown in wireframe and CPK coloring). The catalytic domain is blue and the calcium activation domain (CAD) is gold. In the kinase domain, ANP sits in the catalytic cleft between the large and small lobes of the domain. CAD is bound to the side of the kinase opposite to the catalytic cleft, making it available for peptide substrate binding. | |'''Right scene''' - The crystal structure [[3hx4]] shows the '''active conformation''' of the kinase that is bound to calcium (green spheres) and the ATP analog ANP (also called AMPPNP; shown in wireframe and CPK coloring). The catalytic domain is blue and the calcium activation domain (CAD) is gold. In the kinase domain, ANP sits in the catalytic cleft between the large and small lobes of the domain. CAD is bound to the side of the kinase opposite to the catalytic cleft, making it available for peptide substrate binding. | ||
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| <applet load='3ku2' size='400' frame='true' align='left' caption='3ku2 - inactive TgCDPK1' scene = '55/559103/Holo-ikinase/5' /><br>'''3ku2 scenes''' <Br><scene name='55/559103/Holo-ikinase_cad_rainbow/2'>1. Apo CAD</scene>shown in rainbow colors from the N-terminal (blue) to the C-terminal (red) ends of the domain. <br><scene name='55/559103/Holo-ikinase_cad_rainbow/3'>2. CAD helices</scene><br><scene name='55/559103/Holo-ikinase_cad_rainbow/4'>3. dummy</scene> | | <applet load='3ku2' size='400' frame='true' align='left' caption='3ku2 - inactive TgCDPK1' scene = '55/559103/Holo-ikinase/5' /><br>'''3ku2 scenes''' <Br><scene name='55/559103/Holo-ikinase_cad_rainbow/2'>1. Apo CAD</scene>shown in rainbow colors from the N-terminal (blue) to the C-terminal (red) ends of the domain. <br><scene name='55/559103/Holo-ikinase_cad_rainbow/3'>2. Apo CAD helices</scene><br><scene name='55/559103/Holo-ikinase_cad_rainbow/4'>3. dummy</scene> | ||
| <applet load='3HX4' size='400' frame='true' align='left' caption='3hx4 - active TgCDPK1' scene = '55/559103/Holo-akinase/2' /><Br>'''3hx4 scenes'''<Br><scene name='55/559103/Holo-akinase_cad_rainbow/1'>1. Calcium-bound CAD</scene><br><scene name='55/559103/Holo-akinase_cad_rainbow/2'>2. CAD bent helices</scene><br><scene name='55/559103/Holo-akinase_cad_rainbow/3'>3. dummy</scene> | | <applet load='3HX4' size='400' frame='true' align='left' caption='3hx4 - active TgCDPK1' scene = '55/559103/Holo-akinase/2' /><Br>'''3hx4 scenes'''<Br><scene name='55/559103/Holo-akinase_cad_rainbow/1'>1. Calcium-bound CAD</scene><br><scene name='55/559103/Holo-akinase_cad_rainbow/2'>2. CAD bent helices</scene><br><scene name='55/559103/Holo-akinase_cad_rainbow/3'>3. dummy</scene> | ||
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