User:GomezChristian/sandbox
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Note: Group's draft space -GomezChristian (talk) 21:10, 21 February 2017 (UTC)
Evaluation of Chorismate Mutase Article:
1.Elaboration could be made on conformational trapping of the substrate in the enzyme active site.
2. Figures or schemes to illustrate the catalytic mechanism would aid in visualising the reaction.
3. Further discussion of thermodynamic factors that drive the reaction could be provided.
4. Figure for reaction has a misspelling of chorismate (chromismate). Charles Cole (talk) 21:41, 21 February 2017 (UTC)
Draft:
The conversion of chorismate to prephenate is the first committed step in the pathway to the production of the aromatic amino acids: tyrosine and phenylalanine. The presence of chorismate mutase, increases the rate of the reaction a million fold.[1] In the absence of enzyme catalysis this mechanism proceeds as a concerted, but asynchronous step and is an exergonic process. The mechanism for this transformation is formally a Claisen rearrangement, supported by the kinetic and isotopic data reported by Knowles, et al.[2] In the enzyme active site, interactions between specific residues and the substrate restrict conformational degrees of freedom, such that the entropy of activation is effectively reduced to zero, and thereby promotes catalysis. As a result, there is no formal intermediate, but rather a pseudo-diaxial chair-like transition state. Evidence for this conformation is provided by an inverse secondary kinetic isotope effect at the carbon directly attached to the hydroxyl group.[1] This seemingly unfavorable arrangement is achieved through a series of electrostatic interactions, which rotate the extended chain of chorismate into the conformation required for this concerted mechanism.
An additional stabilizing factor in this enzyme-substrate complex is hydrogen bonding between the lone pair of the oxygen in the vinyl ether system and hydrogen bond donor residues. Not only does this stabilize the complex, but disruption of resonance within the vinyl ether destabilizes the ground state and reduces the energy barrier for this transformation. An alternative view is that electrostatic stabilization of the polarized transition state is of great importance in this reaction. This is shown in mutants of the native enzyme in which Arg90 is replaced with citrulline to demonstrate the importance of hydrogen bonding to stabilize the transition state.[3] Other work using chorismate mutase from Bacillus subtilis showed evidence that when a cation was aptly placed in the active site, the electrostatic interactions between it and the negatively charged transition state promoted catalysis.[4]
Additional studies have been done on the near attack conformer (NAC) of the reaction catalyzed by chorismate mutase. This NAC is the reactive conformation of the ground state that is directly converted to the transition state in the enzyme. Using thermodynamic integration (TI) methods, the standard free energies (ΔGN°) for NAC formation were calculated in six different environments. The data obtained suggests that effective catalysis is derived from stabilization of both the NAC and transition state.[5] However, other experimental evidence supports that the NAC effect observed is simply a result of electrostatic transition state stabilization.[6]
Overall, there have been extensive studies on the exact mechanism of this reaction, but the rate-determining step has yet to be uncovered. Some questions that remain surrounding the mechanism are how conformational constraint of the flexible substrate, specific hydrogen bonding to the transition state, and electrostatic interactions actually contribute to catalysis.
Current Mechanism Section:
The mechanism for the transformation of chorismate to prephenate is formally a Claisen rearrangement. This transformation is the first committed step in the pathway to production of the aromatic amino acids: tyrosine and phenylalanine. In the absence of enzyme catalysis this mechanism proceeds as a concerted, but asynchronous step and is an exergonic process. As a result, there is no formal intermediate, but rather a chair-like transition state. The addition of chorismate mutase, increases the rate of the reaction a million fold. There have been extensive studies on the exact mechanism of this reaction, but the rate-determining step has yet to be uncovered. Some questions that remain surrounding the mechanism are how conformational constraint of the flexible substrate, specific hydrogen bonding to the transition state, and electrostatic interactions actually contribute to catalysis. One study using CM from B. subtilis showed evidence that when a cation was aptly placed in the active site, the electrostatic interactions between it and the negatively charged transition state promoted catalysis.
GomezChristian (talk) 23:04, 26 February 2017 (UTC)
- ^ a b Lee, Ay; Stewart, J.D.; Clardy, J.; Ganem, B. "New insight into the catalytic mechanism of chorismate mutases from structural studies". Chemistry & Biology. 2 (4): 195–203. doi:10.1016/1074-5521(95)90269-4.
- ^ Gray, Joseph V.; Knowles, Jeremy R. (1994-08-01). "Monofunctional Chorismate Mutase from Bacillus subtilis: FTIR Studies and the Mechanism of Action of the Enzyme". Biochemistry. 33 (33): 9953–9959. doi:10.1021/bi00199a018. ISSN 0006-2960.
- ^ Kienhöfer, Alexander; Kast, Peter; Hilvert, Donald (2003-03-01). "Selective Stabilization of the Chorismate Mutase Transition State by a Positively Charged Hydrogen Bond Donor". Journal of the American Chemical Society. 125 (11): 3206–3207. doi:10.1021/ja0341992. ISSN 0002-7863.
- ^ Kast, Peter; Grisostomi, Corinna; Chen, Irene A.; Li, Songlin; Krengel, Ute; Xue, Yafeng; Hilvert, Donald (2000-11-24). "A Strategically Positioned Cation Is Crucial for Efficient Catalysis by Chorismate Mutase". Journal of Biological Chemistry. 275 (47): 36832–36838. doi:10.1074/jbc.M006351200. ISSN 0021-9258. PMID 10960481.
{{cite journal}}: CS1 maint: unflagged free DOI (link) - ^ Hur, Sun; Bruice, Thomas C. (2003-10-14). "The near attack conformation approach to the study of the chorismate to prephenate reaction". Proceedings of the National Academy of Sciences. 100 (21): 12015–12020. doi:10.1073/pnas.1534873100. ISSN 0027-8424. PMC 218705. PMID 14523243.
{{cite journal}}: CS1 maint: PMC format (link) - ^ Štrajbl, Marek; Shurki, Avital; Kato, Mitsunori; Warshel, Arieh (2003-08-01). "Apparent NAC Effect in Chorismate Mutase Reflects Electrostatic Transition State Stabilization". Journal of the American Chemical Society. 125 (34): 10228–10237. doi:10.1021/ja0356481. ISSN 0002-7863.