User:Alice Harmon/Sandbox 2: Difference between revisions

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 cellular responses to many 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>, and they are targets for the development of drugs to fight parasitic infections <ref>PMID:20436472</ref>.

CDPKs are monomeric enzymes containing an amino-terminal [[Eukaryotic Protein Kinase Catalytic Domain]] linked to a carboxy-terminal calcium-binding regulatory domain that contains four [[EF hand]] calcium-binding sites. The protein kinase domain is similar in sequence to members of the calmodulin-dependent protein kinase family<ref>PMID:1852075</ref>, and the calcium-binding domain has sequence similarity to [[calmodulin]]. CDPKs are regulated by the binding of Ca²⁺ to the regulatory domain (called the calcium activation domain or CAD), and they 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 conformation changes that occur upon the binding of calcium to the regulatory domain <ref> PMID:20436473 </ref>. In the default scenes of the inactive (apo CDPK) and active (Ca²⁺-bound CDPK) structures below it is easy to see the change in position of the CAD relative to the protein kinase domain. The internal structures of both domains are also affected.  To compare the two structures click on pairs of green links that have the same number.  

|'''Left scene''' - The crystal structure [[3ku2]] shows the '''inactive conformation''' of the kinase that is bound to 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. Note the long α-helices of the CAD which span across the catalytic cleft (marked by the bound ANP) blocking it from binding peptide substrate.  

|'''Right scene''' - The crystal structure [[3hx4]] shows the '''active conformation''' of the kinase that is bound to four calcium ions (green spheres), each bound to an [[EF hand]]. As in the left scene the catalytic domain is blue and the CAD is gold, and the ATP analog ANP is shown in wireframe and CPK coloring. In these default still scenes the large lobe of the kinase domain is in approximately the same orientation. Calcium-bound CAD interacts with the side of the kinase domain that is opposite from the catalytic cleft, making it available for peptide substrate binding.

| <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/5'>1. Default scene</scene><Br><scene name='55/559103/Holo-ikinase_cad_rainbow/2'>2. Apo CAD</scene> shown in rainbow colors starting with blue at the N-terminal end to red at the C-terminal end of the domain. <br><scene name='55/559103/Holo-ikinase_cad_rainbow/3'>3. Apo CAD helices</scene> are long and straight.<br><scene name='55/559103/Kd_critical/5'>4. Inactive kinase domain critical structures</scene>: ATP binding loop in lime; Subdomain III in orchid; catalytic loop in blue; Mg2+ loop/activation loop in gold.  

| <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/2'>1. Default Scene</scene><Br><scene name='55/559103/Holo-akinase_cad_rainbow/1'>2. Calcium-bound CAD</scene> is more compact as a result of rearrangement of secondary structures.<br><scene name='55/559103/Holo-akinase_cad_rainbow/2'>3. Calcium-bound CAD helices</scene> are each broken into horseshoe shapes.<br><scene name='55/559103/Akd_critical/5'>4. Active kinase domain critical structures</scene> are in the same color scheme as in the left scene, and the large lobe is in approximately the same orientation. Note the large change in the activation loop (gold). In the small lobe there is a  change in shape and position of the ATP-binding loop (green) and ANP (CPK), and there is extension and change in position of subdomain III (orchid). These latter changes indicates twisting of the small lobe relative to the large lobe.

== 3D Structures of calcium-dependent protein kinase (CDPK) ==

 

[[3nyv]] – TgCDPK+WHI-P180 – ''Toxoplasma gondii''<br />

[[1s6i]] - sCDPK α chain A C-terminal+CaM-like domain<br />