Sandbox Reserved 792

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<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]
<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]
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The <scene name='56/563204/Secondary_structure/2'>secondary structure</scene> shows the 23 alpha helices (blue-gray) comprise the vast majority of the protein. In contrast, there is only one small anti-parallel beta sheet (orange) per subunit.
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The <scene name='56/563204/Secondary_structure/2'>secondary structure</scene> shows the 23 alpha helices (blue-gray) comprise the vast majority of each of the protein subunits. In contrast, there is only one small anti-parallel beta sheet (orange) per subunit. Not surprisingly, [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=1csc&template=protein.html&o=RESCONS&l=1&chain=A&c=999&r=wiring| PBDsum] further indicates the numerous helices interact with each other extensively, with 50 helix-helix interactions per chain.
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.
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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.
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The <scene name='56/563204/Hydrophobic_residues/1'>hydrophobic residues</scene> are shown in grey, and the <scene name='56/563204/Charged_and_polar_residues/2'>hydrophilic residues</scene> are in pink. The ligand is shown in purple.
== Solvent Interaction ==
== Solvent Interaction ==
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The <scene name='56/563204/Water_interaction/1'>water molecule interactions</scene> 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 <scene name='56/563204/Dimer_water_and_ligand/2'>dimer</scene>.
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The <scene name='56/563204/Water_interaction/1'>water molecule interactions</scene> are shown in blue, the protein in cream and the ligand in a light purple. The A chain can be seen to be more heavily solvated on the side opposite the beta sheet, implying that the side with the beta sheet is where the two monomers join to form the fully functional protein. Indeed, the water interaction (with the same color designations) in the <scene name='56/563204/Dimer_water_and_ligand/2'>dimer</scene> (same colors used) indicates this binding location to be the case and the protein to be fairly equally solvated around the entirety of the protein.
== Active Site ==
== Active Site ==
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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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The <scene name='56/563204/Ligand_interaction/1'>ligand binding residues</scene> are depicted in ball in stick fashion while the rest of the protein is depicted as a ribbon diagram. The <scene name='56/563204/Ligand_interaction/2'>ligand itself</scene> (Acetyl-CoA, water and oxaloacetate) is shown in pink. The <scene name='56/563204/Catalytic_residues/1'>catalytic residues</scene>, D375, H274, H320 and S244, [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=1csc&template=protein.html&o=RESCONS&l=1&chain=A&c=999&r=wiring| PBDsum] are shown in black.
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== Mechanism of Action ==
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==Mechanism of Action==
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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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The condensation reaction (Acetyl-CoA + H2O + oxaloacetate = citrate + CoA) 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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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]
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]
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3. [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=1csc&template=protein.html&o=RESCONS&l=1&chain=A&c=999&r=wiring| PBDsum]

Revision as of 00:53, 18 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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Citrate Synthase

Drag the structure with the mouse to rotate


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 23 alpha helices (blue-gray) comprise the vast majority of each of the protein subunits. In contrast, there is only one small anti-parallel beta sheet (orange) per subunit. Not surprisingly, PBDsum further indicates the numerous helices interact with each other extensively, with 50 helix-helix interactions per chain.

The in the backbone are shown in green.

The are shown in grey, and the are in pink. The ligand is shown in purple.

Solvent Interaction

The are shown in blue, the protein in cream and the ligand in a light purple. The A chain can be seen to be more heavily solvated on the side opposite the beta sheet, implying that the side with the beta sheet is where the two monomers join to form the fully functional protein. Indeed, the water interaction (with the same color designations) in the (same colors used) indicates this binding location to be the case and the protein to be fairly equally solvated around the entirety of the protein.

Active Site

The are depicted in ball in stick fashion while the rest of the protein is depicted as a ribbon diagram. The (Acetyl-CoA, water and oxaloacetate) is shown in pink. The , D375, H274, H320 and S244, PBDsum are shown in black.

Mechanism of Action

The condensation reaction (Acetyl-CoA + H2O + oxaloacetate = citrate + CoA) 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

3. PBDsum

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