Citrate Synthase: Difference between revisions
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<table align = 'left' cellpadding='0'><tr><td rowspan='2'> </td><td bgcolor='#9999ff'><StructureSection load='Image:5ctsBIOL.pdb.gz' size='380' side='right' scene='Citrate_Synthase/5ctsactivesite/ | <table align = 'left' cellpadding='0'><tr><td rowspan='2'> </td><td bgcolor='#9999ff'><StructureSection load='Image:5ctsBIOL.pdb.gz' size='380' side='right' scene='Citrate_Synthase/5ctsactivesite/3' caption='Citrate synthase catalysis in the closed conformation'> | ||
'''Mechanism:''' <scene name='Citrate_Synthase/5ctsactivesitedimer/2'>Three side chains in each of the two active sites</scene> of the dimer contribute directly to the chemistry of catalysis. Focusing on a single active site in the closed conformation, one can easily observe that <scene name='Citrate_Synthase/5ctsactivesiteresidues/10'>these three side chains and the two substrates are together</scene> in an arrangement favorable for reaction. (By contrast, <scene name='Citrate_Synthase/Activesite1ctsto2cts/12'>the active site residues are significantly farther apart</scene> in the open conformation; the difference in the distance is ~5Å along the axis that changes the most during the conformation shift.) {{Link Toggle AnimationOnPause}} | '''Mechanism:''' <scene name='Citrate_Synthase/5ctsactivesitedimer/2'>Three side chains in each of the two active sites</scene> of the dimer contribute directly to the chemistry of catalysis. Focusing on a single active site in the closed conformation, one can easily observe that <scene name='Citrate_Synthase/5ctsactivesiteresidues/10'>these three side chains and the two substrates are together</scene> in an arrangement favorable for reaction. (By contrast, <scene name='Citrate_Synthase/Activesite1ctsto2cts/12'>the active site residues are significantly farther apart</scene> in the open conformation; the difference in the distance is ~5Å along the axis that changes the most during the conformation shift.) {{Link Toggle AnimationOnPause}} | ||
The reaction mechanism for citrate synthase was proposed by Remington and colleagues<ref name="1cts">PMID:7120407</ref><ref>PMID: 2337600</ref> and is illustrated here in three dimensions using structures resembling key states of the reaction<ref>[[5cts]] as the state preceding condensation with oxaloacetate and a non-reactive version of acetyl-CoA bound, [[6cts]] as the state containing the bound intermediate, and [[3cts]] as the complex with the products. Positions of hydrogens on the ligands were calculated and added back to structures in the reaction scheme for instructional purposes and are not present in the experimentally-determined structures; additionally, arrows are drawn with atoms of the analog of acetyl-CoA to approximate the position of the reactive groups only as the reactive groups are not actually part of the analog or the molecules would have reacted; please, see the reaction scheme on this page for a more thorough accounting of the chemistry.</ref>. In this mechanism, three ionizable side chains in the active site of citrate synthase participate in acid-base catalysis: <scene name='Citrate_Synthase/5ctsactivesiteresidues/10'>His 274, His 320, and Asp 375</scene>. Citrate synthase is among one of the few enzymes that can directly form a carbon-carbon bond without the presence of metal ion cofactors.<br> | The reaction mechanism for citrate synthase was proposed by Remington and colleagues<ref name="1cts">PMID:7120407</ref><ref>PMID: 2337600</ref> and is illustrated here in three dimensions using structures resembling key states of the reaction<ref>[[5cts]] as the state preceding condensation with oxaloacetate and a non-reactive version of acetyl-CoA bound, [[6cts]] as the state containing the bound intermediate, and [[3cts]] as the complex with the products. Positions of hydrogens on the ligands were calculated and added back to structures in the reaction scheme for instructional purposes and are not present in the experimentally-determined structures; additionally, arrows are drawn with atoms of the analog of acetyl-CoA to approximate the position of the reactive groups only as the reactive groups are not actually part of the analog or the molecules would have reacted; please, see the reaction scheme on this page for a more thorough accounting of the chemistry.</ref>. In this mechanism, three ionizable side chains in the active site of citrate synthase participate in acid-base catalysis: <scene name='Citrate_Synthase/5ctsactivesiteresidues/10'>His 274, His 320, and Asp 375</scene>. Citrate synthase is among one of the few enzymes that can directly form a carbon-carbon bond without the presence of metal ion cofactors.<br> | ||
Revision as of 17:14, 23 June 2011
The Structure and Mechanism of Citrate Synthase
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Citrate synthase is an enzyme active in all examined cells, where it is most often responsible for catalyzing the first reaction of the 3cts: the condensation of acetyl-CoA and oxaloacetate to form citrate. Although in eukaryotes it is a mitochondrial enzyme, and in fact, is often used as a enzyme marker for intact mitochondria, it is encoded by nuclear DNA[1]. The standard free energy change (ΔG°’) for the citrate synthase reaction is -31.5kJ/mol [2]. This negative free energy value means that citrate synthase is likely to function far from equilibrium under physiological conditions, and is thus a rate-determining enzyme in the citric acid cycle.
Structure: Biologically, citrate synthase exists as a
homodimer of a single amino acid chain monomer. Each identical subunit consists of a large and a small domain, and is comprised almost entirely of α helices (making it an all α protein). In its free enzyme state, citrate synthase exists in an “open” form of the homodimer, with its two domains forming a cleft containing the substrate (oxaloacetate) binding site (PDB: 1cts) [3][4]. When oxaloacetate binds, the smaller domain undergoes an 18° rotation, sealing the oxaloacetate binding site[5] and resulting in the closed conformation of the homodimer (PDB: 2cts)[3]. The dramatic conformational change is best illustrated via a morph between the "open" and "closed" states, and be sure to view the morph from the side as well to get a full sense of the structural change. The conformational change not only prevents solvent from reaching the bound substrate, but also generates the acetyl-CoA binding site. This presence of “open” and “closed” forms results in citrate synthase having Ordered Sequential kinetic behavior [2].
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Literature and Notes
- ↑ "Citrate Synthase -." Wikipedia, the Free Encyclopedia. Web. 22 Mar. 2010.
- ↑ 2.0 2.1 Voet, Donald, Judith G. Voet, and Charlotte W. Pratt. Fundamentals of Biochemistry: Life at the Molecular Level. Hoboken, NJ: Wiley, 2008.
- ↑ 3.0 3.1 Remington S, Wiegand G, Huber R. Crystallographic refinement and atomic models of two different forms of citrate synthase at 2.7 and 1.7 A resolution. J Mol Biol. 1982 Jun 15;158(1):111-52. PMID:7120407
- ↑ In this structure 5cts, citrate, the resulting product of the conversion, is actually bound where oxaloacetate binds.
- ↑ Bayer E, Bauer B, Eggerer H. Evidence from inhibitor studies for conformational changes of citrate synthase. Eur J Biochem. 1981 Nov;120(1):155-60. PMID:7308213
3D structures of Citrate Synthase
Update June 2011
3msu – CitS – Francisella tularensis
3enj – CitS – Wild boar
2p2w – CitS – Thermotoga maritima
2c6x – CitS residues 2-364 – Bacillus subtilis
3l96, 1owc, 1nxe – EcCitS (mutant) – Eschericia coli
1k3p – EcCitS II
2ibp – CitS – Pyrobaculum aerophilum
1iom, 1ixe – CitS – Thermus thermophilus
1o7x – CitS – Sulfolobus solfataricus
1a59 – CitS – Antarctic bacterium
1aj8 – CitS - Pyrococcus furiosus
5csc, 3cts – cCitS – chicken
1cts, 2cts – pCitS - pig
Citrate synthase binary complex
3l97 - EcCitS (mutant) + S-carboxymethyl-CoA
2r9e – TaCitS + citryl dethia CoA – Thermoplasma acidophilum
6cts – cCitS + citryl thioether CoA
3l98, 1owb, 1nxg - EcCitS (mutant) + NADH
3l99 - EcCitS (mutant) + oxaloacetate
2ifc - TaCitS + oxaloacetate
Citrate synthase ternary complex
2r26 - TaCitS + oxaloacetate + S-carboxymethyl-CoA
2h12 - CitS + oxaloacetate + carboxymethyl dethia-CoA – Acetobacter aceti
1al6, 1csr, 1css, 1csh, 1csi - cCitS + oxaloacetate + carboxymethyl dethia-CoA derivative
5cts - cCitS + oxaloacetate + carboxymethyl CoA
1amz - cCitS + malate + nitromethyl dethia-CoA
1csc, 2csc, 3csc, 4csc - cCitS + malate + carboxymethyl CoA
6csc - cCitS + citrate + trifluoroacetonyl-CoA
4cts - pCitS + oxaloacetate + S-acetonyl CoA
See Also
External Resources
- Citrate Synthase: September 2007 Molecule of the Month as part of the series of tutorials that are at the RCSB Protein Data Bank and written by David Goodsell
- An interactive schematic animation of Citrate synthase's reaction mechanism from Lehninger's Principles of Biochemistry
- Citrate Synthase at Wikipedia
Proteopedia Page Contributors and Editors (what is this?)
Wayne Decatur, Daniel Eddelman, David Canner, Angel Herraez, Eric Martz, Joel L. Sussman, Alexander Berchansky, Michal Harel
