Anthony Noles Sandbox
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=Aconitase= | =Aconitase= | ||
| - | Aconitase (PDB [[7acn]]) catalyzes the reversible isomerization of citrate and isocitrate.The <scene name='Anthony_Noles_Sandbox/Secondary_structure/1'>secondary structure</scene> consists of numerous alternating alpha helices and beta sheets. The tertiary structure is bilobed with the active site in the middle, and, since there is only one subunit, there is no quaternary structure. | + | Aconitase (PDB [[7acn]]) catalyzes the reversible isomerization of citrate and isocitrate.The <scene name='Anthony_Noles_Sandbox/Secondary_structure/1'>secondary structure</scene> consists of numerous alternating alpha helices and beta sheets (α/β alternating). The tertiary structure is somewhat bilobed with the active site in the middle, and, since there is only one subunit, there is no quaternary structure. |
==Mechanism of Aconitase== | ==Mechanism of Aconitase== | ||
{{STRUCTURE_7acn | PDB=7acn | SCENE= }} | {{STRUCTURE_7acn | PDB=7acn | SCENE= }} | ||
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 | + | Substrate-free aconitase contains a [4Fe-4S]2+ cluster with hydroxyl bound to one of the Fe. Upon binding of substrate the bound hydroxyl is protonated. A hydrogen bond from <scene name='Anthony_Noles_Sandbox/His101/1'>His101</scene> to the isocitrate hydroxyl is donated to form water. 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. His167 is also hydrogen bonded to the bound H2O in the [4Fe-4S] cluster. 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. <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> |
| + | Once the substrate, in this case, isocitrate, is bond, the residue which abstracts a proton from the alpha carbon of citrate and isocitrate is <scene name='Anthony_Noles_Sandbox/Ser642/2'>Ser642</scene>. <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> This causes the cis-Aconitate intermediate (seen below), which consists of a double bound, which is a direct result of the deportonation. | ||
====Stage 1: Dehydration==== | ====Stage 1: Dehydration==== | ||
Revision as of 06:30, 1 March 2010
Contents |
Aconitase
Aconitase (PDB 7acn) catalyzes the reversible isomerization of citrate and isocitrate.The consists of numerous alternating alpha helices and beta sheets (α/β alternating). The tertiary structure is somewhat bilobed with the active site in the middle, and, since there is only one subunit, there is no quaternary structure.
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 one of the Fe. Upon binding of substrate the bound hydroxyl is protonated. A hydrogen bond from to the isocitrate hydroxyl is donated to form water. Alternatively, the proton could be donated by as this histidine is hydrogen bonded to a H2O molecule. His167 is also hydrogen bonded to the bound H2O in the [4Fe-4S] cluster. 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. [3] Once the substrate, in this case, isocitrate, is bond, the residue which abstracts a proton from the alpha carbon of citrate and isocitrate is . [4] This causes the cis-Aconitate intermediate (seen below), which consists of a double bound, which is a direct result of the deportonation.
Stage 1: Dehydration
First, dehydration of citrate causes a proton and OH group to be removed from only the 'lower arm'.[5] This forms a cis-Aconitate intermediate.
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. [6]
Thus, the overall reaction that aconitase catalyzes is: Citrate ←→cis-Aconitate←→Isocitrate, as seen below: Image:Catalysis.jpg
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.
- ↑ Beinert, H., Kennedy, M. C., Stout, C.D. “Aconitase as Iron−Sulfur Protein, Enzyme, and Iron-Regulatory Protein.” Chem. Rev. 1996, 96, 2335−2373.
- ↑ 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.
