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From Proteopedia
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You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue. | You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue. | ||
| - | == Introduction == | + | == Introduction and function == |
| - | == Structure of the | + | == Structure of the Caspase-7 == |
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| + | To understand the structure of the Caspase-7, it needs to understand the one of its zymogen, the Procaspase-7. | ||
In the cytoplasm, caspases are not already, constitutively present in their active form. They exist as free cytoplasmic inactive precursors called procaspases. | In the cytoplasm, caspases are not already, constitutively present in their active form. They exist as free cytoplasmic inactive precursors called procaspases. | ||
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Procaspase-7 is a homodimeric globular-303 amino-acids long polypeptide. This protein contains <scene name='60/604484/Two_monomers/1'>two monomers</scene>, representing two catalytic units. Each of these monomers is composed by a central 6-stranded β-sheet and 5 α-helices, forming a <scene name='60/604484/Large_subunit_of_a_monomer/2'>large (20kDa)</scene> and a <scene name='60/604484/Small_subunit_of_a_monomer/2'>small (11kDa)</scene> subunit, linked by a <scene name='60/604484/Interdomain_of_a_monomer/2'>highly flexible interdomain</scene>. The homodimerization is performed thanks to hydrophobic interactions between the 6 β-strands of each monomer. This homodimer is organized in a “open α/β barrel fold”. | Procaspase-7 is a homodimeric globular-303 amino-acids long polypeptide. This protein contains <scene name='60/604484/Two_monomers/1'>two monomers</scene>, representing two catalytic units. Each of these monomers is composed by a central 6-stranded β-sheet and 5 α-helices, forming a <scene name='60/604484/Large_subunit_of_a_monomer/2'>large (20kDa)</scene> and a <scene name='60/604484/Small_subunit_of_a_monomer/2'>small (11kDa)</scene> subunit, linked by a <scene name='60/604484/Interdomain_of_a_monomer/2'>highly flexible interdomain</scene>. The homodimerization is performed thanks to hydrophobic interactions between the 6 β-strands of each monomer. This homodimer is organized in a “open α/β barrel fold”. | ||
| - | Four loops (L1 to L4), located at the two opposite ends of the | + | Four loops (L1 to L4), located at the two opposite ends of the β–sheet, emanate from each homodimer and define the shape of the catalytic groove of each monomer. |
<scene name='60/604484/Position_of_the_l2_loops/3'>L2 interdomain loop</scene> links the two the large and small subunit of each procaspase-7 monomer. In the procaspase-7, this loop is in a “closed” conformation that precludes any possibility of substrate or inhibitor binding to the yet incomplete active site. Thus, in this considered conformation, the enzyme is yet inactive. This highly flexible loop contains two cleavage sites (Asp198 - Asp207) which are essential to the maturation of the Procaspase-7 (cf MATURATION). It also contains an essential residue needed for the catalytic activity of the Caspase-7 : <scene name='60/604484/Position_of_cys186/3'>Cys186</scene> | <scene name='60/604484/Position_of_the_l2_loops/3'>L2 interdomain loop</scene> links the two the large and small subunit of each procaspase-7 monomer. In the procaspase-7, this loop is in a “closed” conformation that precludes any possibility of substrate or inhibitor binding to the yet incomplete active site. Thus, in this considered conformation, the enzyme is yet inactive. This highly flexible loop contains two cleavage sites (Asp198 - Asp207) which are essential to the maturation of the Procaspase-7 (cf MATURATION). It also contains an essential residue needed for the catalytic activity of the Caspase-7 : <scene name='60/604484/Position_of_cys186/3'>Cys186</scene> | ||
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| - | == | + | == Comparison with the Caspase-3 == |
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This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes. | This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes. | ||
Revision as of 23:52, 8 January 2015
Your Heading Here (maybe something like 'Structure')
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References
- ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
- ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
