User:Alice Harmon/Sandbox 2: Difference between revisions

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==CDPK==

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 calcium to the regulatory domain, ~~and~~ thus are activated in processes that elevate the concentration of calcium inside cells.

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 calcium ions 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.

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| <applet load='3HX4' size='400' frame='true' align='left' caption='3hx4 - active TgCDPK1' scene = '55/559103/Holo-akinase/2' /> '''3hx4 scenes''' <scene name='55/559103/Holo-akinase_cad_rainbow/1'>1. Calcium-bound CAD</scene> <scene name='55/559103/Holo-akinase_cad_rainbow/2'>2. CAD bent helices</scene> <scene name='55/559103/Holo-akinase_cad_rainbow/3'>3. dummy</scene>

|}

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

Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}

[[3nyv]] – TgCDPK+WHI-P180 – ''Toxoplasma gondii''

[[3n51]] - TgCDPK CBD +RM-1-95

[[3i7b]] - TgCDPK CBD+ NM-PP1

[[3i7c]] - TgCDPK CBD+ NA-PP2

[[3ku2]] - TgCDPK CBD

[[3khe]], [[3i79]], [[3hzt]] – TgCaMK

[[3hx4]] – TgCDPK+Ca

[[3dxn]] – TgCDPK kinase domain

[[3mwu]] – CpCDPK CBD (mutant)+RM-1-95 – ''Cryptosporidium parvum''

[[3ncg]] - CpCDPK CBD + NM-PP1

[[3lij]] – CpCDPK+Ca

[[3l19]], [[3igo]], [[3hko]] – CpCDPK

[[2qg5]] – CpCDPK chains A, B, D

[[3f3z]] – CpCDPK kinase domain+indirubin_E804

[[3dfa]] - CpCDPK kinase domain

[[2aao]] – CeCDPK chains A, B – ''Arabidopsis thaliana''

[[1iq5]] – CeCDPK CBD+XlCaM – ''Xenopus laevis''

[[1s6j]] – sCDPK α chain A N-terminal – soybean

[[1s6i]] - sCDPK α chain A C-terminal+CaM-like domain

=References=

@@ Line 1: / Line 1: @@
 ==CDPK==
-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 calcium to the regulatory domain, and thus are activated in processes that elevate the concentration of calcium inside cells.
+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 calcium ions 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.
@@ Line 15: / Line 15: @@
 | <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>
 |}
+== 3D Structures of calcium-dependent protein kinase (CDPK) ==
+Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
+[[3nyv]] – TgCDPK+WHI-P180 – ''Toxoplasma gondii''<br />
+[[3n51]] - TgCDPK CBD +RM-1-95<br />
+[[3i7b]] - TgCDPK CBD+ NM-PP1<br />
+[[3i7c]] - TgCDPK CBD+ NA-PP2<br />
+[[3ku2]] - TgCDPK CBD<br />
+[[3khe]], [[3i79]], [[3hzt]] – TgCaMK<br />
+[[3hx4]] – TgCDPK+Ca<br />
+[[3dxn]] – TgCDPK kinase domain<br />
+[[3mwu]] – CpCDPK CBD (mutant)+RM-1-95 – ''Cryptosporidium parvum''<br />
+[[3ncg]] - CpCDPK CBD + NM-PP1<br />
+[[3lij]] – CpCDPK+Ca<br />
+[[3l19]], [[3igo]], [[3hko]] – CpCDPK<br />
+[[2qg5]] – CpCDPK chains A, B, D<br />
+[[3f3z]] – CpCDPK kinase domain+indirubin_E804<br />
+[[3dfa]] - CpCDPK kinase domain<br />
+[[2aao]] – CeCDPK chains A, B – ''Arabidopsis thaliana''<br />
+[[1iq5]] – CeCDPK CBD+XlCaM – ''Xenopus laevis''<br />
+[[1s6j]] – sCDPK α chain A N-terminal – soybean<br />
+[[1s6i]] - sCDPK α chain A C-terminal+CaM-like domain<br />
 =References=