User:Alice Harmon/Sandbox 2

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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[1][2], and they are involved in cellular responses to many stimuli such as hormones and environmental stress[3]. 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 [4][5], and they are targets for the development of drugs to fight parasitic infections [6].

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[7], 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 [8]. 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.

3ku2 - inactive TgCDPK1

Drag the structure with the mouse to rotate

3ku2 scenes

shown in rainbow colors starting with blue at the N-terminal end to red at the C-terminal end of the domain.
are long and straight.
: ATP binding loop in lime; Subdomain III in orchid; catalytic loop in blue; Mg2+ loop/activation loop in gold.

3hx4 - active TgCDPK1

Drag the structure with the mouse to rotate

3hx4 scenes

is more compact as a result of rearrangement of secondary structures.
are each broken into horseshoe shapes.
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)

Updated on 24-September-2013

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

  1. ↑ Hrabak EM, Chan CW, Gribskov M, Harper JF, Choi JH, Halford N, Kudla J, Luan S, Nimmo HG, Sussman MR, Thomas M, Walker-Simmons K, Zhu JK, Harmon AC. The Arabidopsis CDPK-SnRK superfamily of protein kinases. Plant Physiol. 2003 Jun;132(2):666-80. PMID:12805596 doi:10.1104/pp.102.011999
  2. ↑ Asano T, Tanaka N, Yang G, Hayashi N, Komatsu S. Genome-wide identification of the rice calcium-dependent protein kinase and its closely related kinase gene families: comprehensive analysis of the CDPKs gene family in rice. Plant Cell Physiol. 2005 Feb;46(2):356-66. Epub 2005 Feb 2. PMID:15695435 doi:10.1093/pcp/pci035
  3. ↑ Schulz P, Herde M, Romeis T. Calcium-dependent protein kinases: hubs in plant stress signaling and development. Plant Physiol. 2013 Sep 6. PMID:24014579 doi:10.1104/pp.113.222539
  4. ↑ McCoy JM, Whitehead L, van Dooren GG, Tonkin CJ. TgCDPK3 regulates calcium-dependent egress of Toxoplasma gondii from host cells. PLoS Pathog. 2012;8(12):e1003066. doi: 10.1371/journal.ppat.1003066. Epub 2012, Dec 4. PMID:23226109 doi:10.1371/journal.ppat.1003066
  5. ↑ Dvorin JD, Martyn DC, Patel SD, Grimley JS, Collins CR, Hopp CS, Bright AT, Westenberger S, Winzeler E, Blackman MJ, Baker DA, Wandless TJ, Duraisingh MT. A plant-like kinase in Plasmodium falciparum regulates parasite egress from erythrocytes. Science. 2010 May 14;328(5980):910-2. doi: 10.1126/science.1188191. PMID:20466936 doi:10.1126/science.1188191
  6. ↑ Ojo KK, Larson ET, Keyloun KR, Castaneda LJ, Derocher AE, Inampudi KK, Kim JE, Arakaki TL, Murphy RC, Zhang L, Napuli AJ, Maly DJ, Verlinde CL, Buckner FS, Parsons M, Hol WG, Merritt EA, Van Voorhis WC. Toxoplasma gondii calcium-dependent protein kinase 1 is a target for selective kinase inhibitors. Nat Struct Mol Biol. 2010 May;17(5):602-7. Epub 2010 May 2. PMID:20436472 doi:10.1038/nsmb.1818
  7. ↑ Harper JF, Sussman MR, Schaller GE, Putnam-Evans C, Charbonneau H, Harmon AC. A calcium-dependent protein kinase with a regulatory domain similar to calmodulin. Science. 1991 May 17;252(5008):951-4. PMID:1852075
  8. ↑ Wernimont AK, Artz JD, Finerty P Jr, Lin YH, Amani M, Allali-Hassani A, Senisterra G, Vedadi M, Tempel W, Mackenzie F, Chau I, Lourido S, Sibley LD, Hui R. Structures of apicomplexan calcium-dependent protein kinases reveal mechanism of activation by calcium. Nat Struct Mol Biol. 2010 May;17(5):596-601. Epub 2010 May 2. PMID:20436473 doi:10.1038/nsmb.1795

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Alice Harmon

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