Anthony Noles Sandbox
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Aconitase contains <scene name='Anthony_Noles_Sandbox/Fe-scluster/1'>4Fe-4S iron-sulfur cluster</scene>. This iron sulfur cluster does not participate in redox as most do, but coordinates the OH goup of citrate to facilitate its elimination.<ref>PMID:16407072 </ref> It is as this 4Fe-4S site that catalysis occurs and citrate or <scene name='Anthony_Noles_Sandbox/Fe-scluster_bound_isocitrate/1'>isocitrate</scene> is bound. The rest of the <scene name='Anthony_Noles_Sandbox/Fe-scluster_w_active_site/2'>active site</scene> is made up of residues Gln72, Asp100, His101, Asp165, Ser166, His167, His147, Glu262, Asn258, Cys358, Cys421, Cys424, Cys358, Cys421, Asn446, Arg447, Arg452, Asp568, Ser642, Ser643, Arg644, Arg580. <ref>Beinert, H., Kennedy, M. C., Stout, C.D. “Aconitase as Iron−Sulfur Protein, Enzyme, and Iron-Regulatory Protein.” Chem. Rev. 1996, 96, 2335−2373.</ref> | Aconitase contains <scene name='Anthony_Noles_Sandbox/Fe-scluster/1'>4Fe-4S iron-sulfur cluster</scene>. This iron sulfur cluster does not participate in redox as most do, but coordinates the OH goup of citrate to facilitate its elimination.<ref>PMID:16407072 </ref> It is as this 4Fe-4S site that catalysis occurs and citrate or <scene name='Anthony_Noles_Sandbox/Fe-scluster_bound_isocitrate/1'>isocitrate</scene> is bound. The rest of the <scene name='Anthony_Noles_Sandbox/Fe-scluster_w_active_site/2'>active site</scene> is made up of residues Gln72, Asp100, His101, Asp165, Ser166, His167, His147, Glu262, Asn258, Cys358, Cys421, Cys424, Cys358, Cys421, Asn446, Arg447, Arg452, Asp568, Ser642, Ser643, Arg644, Arg580. <ref>Beinert, H., Kennedy, M. C., Stout, C.D. “Aconitase as Iron−Sulfur Protein, Enzyme, and Iron-Regulatory Protein.” Chem. Rev. 1996, 96, 2335−2373.</ref> | ||
| - | Substrate-free aconitase contains a [4Fe-4S]2+ cluster with hydroxyl bound to Fe4. Upon binding of substrate the bound hydroxyl is protonated and the coordination number of Fe4 increases from four to six. A hydrogen bond from <scene name='Anthony_Noles_Sandbox/His101/1'>His101</scene> to the isocitrate hydroxyl suggests that the proton donated to form H2O is derived from this histidine. Alternatively, the proton could be donated by <scene name='Anthony_Noles_Sandbox/His167/1'>His167</scene> as this histidine is hydrogen bonded to a H2O molecule in the [3Fe-4S] form which is closest to the bound hydroxyl in the [4Fe-4S] form. His167 is also hydrogen bonded to the bound H2O in the [4Fe-4S] from. Both <scene name='Anthony_Noles_Sandbox/His_101_and_167/1'>His101 and His167</scene> are paired with carboxylates (<scene name='Anthony_Noles_Sandbox/Asp100_and_glu262/1'>Asp100 and Glu262</scene>, respectively) and are likely to be protonated. As noted, the conformational change associated with substrate binding which reorients the cluster also maintains the position of the hydroxyl/H2O molecule on Fe4 with respect to the histidines. The residue which abstracts a proton from C of citrate and isocitrate is <scene name='Anthony_Noles_Sandbox/Ser642/ | + | Substrate-free aconitase contains a [4Fe-4S]2+ cluster with hydroxyl bound to Fe4. Upon binding of substrate the bound hydroxyl is protonated and the coordination number of Fe4 increases from four to six. A hydrogen bond from <scene name='Anthony_Noles_Sandbox/His101/1'>His101</scene> to the isocitrate hydroxyl suggests that the proton donated to form H2O is derived from this histidine. Alternatively, the proton could be donated by <scene name='Anthony_Noles_Sandbox/His167/1'>His167</scene> as this histidine is hydrogen bonded to a H2O molecule in the [3Fe-4S] form which is closest to the bound hydroxyl in the [4Fe-4S] form. His167 is also hydrogen bonded to the bound H2O in the [4Fe-4S] from. Both <scene name='Anthony_Noles_Sandbox/His_101_and_167/1'>His101 and His167</scene> are paired with carboxylates (<scene name='Anthony_Noles_Sandbox/Asp100_and_glu262/1'>Asp100 and Glu262</scene>, respectively) and are likely to be protonated. As noted, the conformational change associated with substrate binding which reorients the cluster also maintains the position of the hydroxyl/H2O molecule on Fe4 with respect to the histidines. The residue which abstracts a proton from C of citrate and isocitrate is <scene name='Anthony_Noles_Sandbox/Ser642/2'>Ser642</scene>. |
====Stage 1: Dehydration==== | ====Stage 1: Dehydration==== | ||
Revision as of 02:13, 1 March 2010
Contents |
Aconitase
Aconitase (PDB 7acn) catalyzes the reversible isomerization of citrate and isocitrate.
Mechanism of Aconitase
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| 7acn, resolution 2.00Å () | |||||||||
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| Ligands: | , | ||||||||
| Non-Standard Residues: | |||||||||
| Activity: | Aconitate hydratase, with EC number 4.2.1.3 | ||||||||
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
Aconitase contains . This iron sulfur cluster does not participate in redox as most do, but coordinates the OH goup of citrate to facilitate its elimination.[1] It is as this 4Fe-4S site that catalysis occurs and citrate or is bound. The rest of the is made up of residues Gln72, Asp100, His101, Asp165, Ser166, His167, His147, Glu262, Asn258, Cys358, Cys421, Cys424, Cys358, Cys421, Asn446, Arg447, Arg452, Asp568, Ser642, Ser643, Arg644, Arg580. [2]
Substrate-free aconitase contains a [4Fe-4S]2+ cluster with hydroxyl bound to Fe4. Upon binding of substrate the bound hydroxyl is protonated and the coordination number of Fe4 increases from four to six. A hydrogen bond from to the isocitrate hydroxyl suggests that the proton donated to form H2O is derived from this histidine. Alternatively, the proton could be donated by as this histidine is hydrogen bonded to a H2O molecule in the [3Fe-4S] form which is closest to the bound hydroxyl in the [4Fe-4S] form. His167 is also hydrogen bonded to the bound H2O in the [4Fe-4S] from. Both are paired with carboxylates (, respectively) and are likely to be protonated. As noted, the conformational change associated with substrate binding which reorients the cluster also maintains the position of the hydroxyl/H2O molecule on Fe4 with respect to the histidines. The residue which abstracts a proton from C of citrate and isocitrate is .
Stage 1: Dehydration
First, dehydration of citrate causes a proton and OH group to be removed from only the 'lower arm'.[3] This forms a cis-Aconitate intermediate.
Show mechanism here!
Stage 2: Rehydration
The second main stage of the reaction is the rehydration of the cis-Aconitate intermediate. This forms isocitrate. It is catalyzed in a stereospecific way such that only one isocitrate stereoisomer is formed. [4]
Show mechanism here!
Thus, the overall reaction that aconitase catalyzes is:
Show total mechanism here!
References
- ↑ Dupuy J, Volbeda A, Carpentier P, Darnault C, Moulis JM, Fontecilla-Camps JC. Crystal structure of human iron regulatory protein 1 as cytosolic aconitase. Structure. 2006 Jan;14(1):129-39. PMID:16407072 doi:10.1016/j.str.2005.09.009
- ↑ Beinert, H., Kennedy, M. C., Stout, C.D. “Aconitase as Iron−Sulfur Protein, Enzyme, and Iron-Regulatory Protein.” Chem. Rev. 1996, 96, 2335−2373.
- ↑ Voet, Donald, Judith G. Voet, and Charlotte W. Pratt. Fundamentals of Biochemistry Life at the Molecular Level. New York: John Wiley & Sons, 2008. p. 578. Print.
- ↑ Voet, Donald, Judith G. Voet, and Charlotte W. Pratt. Fundamentals of Biochemistry Life at the Molecular Level. New York: John Wiley & Sons, 2008. p. 579. Print.
External Links
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