Sandbox Reserved 792
From Proteopedia
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== Introduction == | == Introduction == | ||
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== Structure == | == Structure == | ||
| - | + | <scene name='56/563204/Citrate_synthase_dimer/1'>Citrate synthase</scene> is a homodimer of its <scene name='56/563204/Chain_a/1'>A chain</scene>. The A chain is comprised of 429 residues, and with a molecular weight of 51.7 kDa. [http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=3&ved=0CD4QFjAC&url=http%3A%2F%2Fwww.oroboros.at%2Ffileadmin%2Fuser_upload%2FMiPNet_Publications%2FMiPNet08.14_CitrateSynthase.pdf&ei=x3ZgUoraCMrq2QWFq4HQCQ&usg=AFQjCNHb4AXCRNgpeQLm7YLW2YSLRztf0Q&bvm=bv.54934254,d.b2I&cad=rja] | |
| - | The <scene name='56/563204/Secondary_structure/2'>secondary structure</scene> shows the vast majority of the protein is alpha helices (blue-gray) with | + | The <scene name='56/563204/Secondary_structure/2'>secondary structure</scene> shows the vast majority of the protein is alpha helices (blue-gray) with one small anti-parallel beta sheet (orange) per subunit. |
The <scene name='56/563204/Backbone_hydrogen_bonds/2'>hydrogen bonds</scene> in the backbone are shown in green. | The <scene name='56/563204/Backbone_hydrogen_bonds/2'>hydrogen bonds</scene> in the backbone are shown in green. | ||
| - | The <scene name='56/563204/Hydrophobic_residues/1'>hydrophobic residues</scene> are shown in grey. The <scene name='56/563204/Charged_and_polar_residues/1'> | + | The <scene name='56/563204/Hydrophobic_residues/1'>hydrophobic residues</scene> are shown in grey. The <scene name='56/563204/Charged_and_polar_residues/1'>hydrophilic residues</scene> are in pink. |
== Solvent Interaction == | == Solvent Interaction == | ||
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== Active Site == | == Active Site == | ||
| - | The <scene name='56/563204/Ligand_interaction/1'>ligand binding residues</scene> are depicted in ball in stick and the rest of the protein is in ribbon diagram. The <scene name='56/563204/Catalytic_residues/1'>catalytic residues</scene> are shown in black. | + | The <scene name='56/563204/Ligand_interaction/1'>ligand binding residues</scene> are depicted in ball in stick and the rest of the protein is in ribbon diagram. The <scene name='56/563204/Ligand_interaction/2'>ligand itself</scene> is shown in pink. The <scene name='56/563204/Catalytic_residues/1'>catalytic residues</scene> are shown in black. |
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== Mechanism of Action == | == Mechanism of Action == | ||
| + | The condensation reaction has been proposed to involve two concerted general acid-base catalysis steps, meaning the catalytic residues serve as the general acids and bases needed. The mechanism is also seen to proceed through an enol (rather than an enolate) intermediate, and exhibit an inversion of sterochemistry at the nucleophilic carbon atom [http://www.ncbi.nlm.nih.gov/pubmed/2337600]. | ||
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| + | == References == | ||
| + | 1. Kuznetsov, A.V., Lassnig, B., Gnaiger, E. (2010). Laboratory Protocol Citrate Synthase Mitochondrial Marker Enzyme. ''Mitochondrial Physiology Network'' 08.14: 1-10.[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=3&ved=0CD4QFjAC&url=http%3A%2F%2Fwww.oroboros.at%2Ffileadmin%2Fuser_upload%2FMiPNet_Publications%2FMiPNet08.14_CitrateSynthase.pdf&ei=x3ZgUoraCMrq2QWFq4HQCQ&usg=AFQjCNHb4AXCRNgpeQLm7YLW2YSLRztf0Q&bvm=bv.54934254,d.b2I&cad=rja| 1] | ||
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| + | 2. Karpusas M, Branchaud B, Remington SJ. (1990). Proposed mechanism for the condensation reaction of citrate synthase: 1.9-A structure of the ternary complex with oxaloacetate and carboxymethyl coenzyme A. ''Biochemistry''. Mar 6;29(9):2213-9. [http://www.ncbi.nlm.nih.gov/pubmed/2337600| 2] | ||
Revision as of 23:58, 17 October 2013
| This Sandbox is Reserved from Oct 10, 2013, through May 20, 2014 for use in the course "CHEM 410 Biochemistry 1 and 2" taught by Hanna Tims at the Messiah College. This reservation includes Sandbox Reserved 780 through Sandbox Reserved 807. |
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Contents |
Introduction
Structure
is a homodimer of its . The A chain is comprised of 429 residues, and with a molecular weight of 51.7 kDa. [1]
The shows the vast majority of the protein is alpha helices (blue-gray) with one small anti-parallel beta sheet (orange) per subunit.
The in the backbone are shown in green.
The are shown in grey. The are in pink.
Solvent Interaction
The are shown in blue, the protein in cream and the ligand in a light purple. The water interaction (with the same color designations) are similar in the .
Active Site
The are depicted in ball in stick and the rest of the protein is in ribbon diagram. The is shown in pink. The are shown in black.
Mechanism of Action
The condensation reaction has been proposed to involve two concerted general acid-base catalysis steps, meaning the catalytic residues serve as the general acids and bases needed. The mechanism is also seen to proceed through an enol (rather than an enolate) intermediate, and exhibit an inversion of sterochemistry at the nucleophilic carbon atom [2].
References
1. Kuznetsov, A.V., Lassnig, B., Gnaiger, E. (2010). Laboratory Protocol Citrate Synthase Mitochondrial Marker Enzyme. Mitochondrial Physiology Network 08.14: 1-10.1
2. Karpusas M, Branchaud B, Remington SJ. (1990). Proposed mechanism for the condensation reaction of citrate synthase: 1.9-A structure of the ternary complex with oxaloacetate and carboxymethyl coenzyme A. Biochemistry. Mar 6;29(9):2213-9. 2
