Aconitase

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aconitate hydratase
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Aconitase family
(aconitate hydratase)
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1aco / SCOPe / SUPFAM
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PDBsumstructure summary

Aconitase (aconitate hydratase;

tricarboxylic acid cycle, a non-redox-active process.[3][4][5]

Structure

Aconitase, displayed in the structures in the right margin of this page, has two slightly different structures, depending on whether it is activated or inactivated.

C-terminal domain.[6] The Fe-S cluster and a SO2−
4
anion also reside in the active site.[6] When the enzyme is activated, it gains an additional iron atom, creating a [4Fe-4S] cluster.[7][8] However, the structure of the rest of the enzyme is nearly unchanged; the conserved atoms between the two forms are in essentially the same positions, up to a difference of 0.1 angstroms.[7]

Function

In contrast with the majority of

iron-sulfur cluster of aconitase reacts directly with an enzyme substrate. Aconitase has an active [Fe4S4]2+ cluster, which may convert to an inactive [Fe3S4]+ form. Three cysteine (Cys) residues have been shown to be ligands of the [Fe4S4] centre. In the active state, the labile iron
ion of the [Fe4S4] cluster is not coordinated by Cys but by water molecules.

The

mRNA turnover (degradation). The specific regulator protein, the IRE-BP, binds to IREs in both 5' and 3' regions, but only to RNA in the apo form, without the Fe-S cluster. Expression of IRE-BP in cultured cells has revealed that the protein functions either as an active aconitase, when cells are iron-replete, or as an active RNA-binding protein, when cells are iron-depleted. Mutant IRE-BPs, in which any or all of the three Cys residues involved in Fe-S formation are replaced by serine
, have no aconitase activity, but retain RNA-binding properties.

Aconitase is inhibited by fluoroacetate, therefore fluoroacetate is poisonous. Fluoroacetate, in the citric acid cycle, is converted to fluorocitrate by citrate synthase. Fluorocitrate competitively inhibits aconitase halting the citric acid cycle.[9] The iron sulfur cluster is highly sensitive to oxidation by superoxide.[10]

Mechanism

Aconitase arrow-pushing mechanism [11][12]
Citrate and the Fe-S cluster in the active site of aconitase: dashed yellow lines show interactions between the substrate and nearby residues[13]

Aconitase employs a dehydration-hydration mechanism.

acetyl CoA, even though these two carbons are equivalent except that one is "pro-R" and the other "pro-S" (see Prochirality).[15]: 393  At this point, the intermediate is rotated 180°.[11] This rotation is referred to as a "flip."[12] Because of this flip, the intermediate is said to move from a "citrate mode" to a "isocitrate mode."[16]

How exactly this flip occurs is debatable. One theory is that, in the

rate-limiting step of the mechanism, the cis-aconitate is released from the enzyme, then reattached in the isocitrate mode to complete the reaction.[16] This rate-limiting step ensures that the right stereochemistry, specifically (2R,3S), is formed in the final product.[16][17] Another hypothesis is that cis-aconitate stays bound to the enzyme while it flips from the citrate to the isocitrate mode.[11]

In either case, flipping cis-aconitate allows the dehydration and hydration steps to occur on opposite faces of the intermediate.[11] Aconitase catalyzes trans elimination/addition of water, and the flip guarantees that the correct stereochemistry is formed in the product.[11][12] To complete the reaction, the serine and histidine residues reverse their original catalytic actions: the histidine, now basic, abstracts a proton from water, priming it as a nucleophile to attack at C2, and the protonated serine is deprotonated by the cis-aconitate double bond to complete the hydration, producing isocitrate.[11]

Isocitrate and the Fe-S cluster in the active site of aconitase[13]PDB: 1C97​;

Family members

Aconitases are expressed in bacteria to humans. Humans express the following two aconitase isozymes:

Chr. 9 p21.1
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StructuresSwiss-model
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Chr. 22 q13.2
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Interactive pathway map

Click on genes, proteins and metabolites below to link to respective articles. [§ 1]

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TCACycle_WP78Go to articleGo to articleGo to articleGo to articleGo to HMDBGo to articleGo to articleGo to articleGo to HMDBGo to HMDBGo to articleGo to WikiPathwaysGo to articleGo to articleGo to articleGo to WikiPathwaysGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to WikiPathwaysGo to articleGo to articleGo to articleGo to HMDBGo to articleGo to articleGo to articleGo to articleGo to articleGo to WikiPathwaysGo to articleGo to WikiPathwaysGo to HMDBGo to articleGo to WikiPathwaysGo to articleGo to HMDBGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to articleGo to article
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TCACycle_WP78 edit
  1. ^ The interactive pathway map can be edited at WikiPathways: "TCACycle_WP78".

References

  1. PMID 1547214
    .
  2. .
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  6. ^ .
  7. ^ .
  8. .
  9. .
  10. .
  11. ^ a b c d e f g h i Takusagawa F. "Chapter 16: Citric Acid Cycle" (PDF). Takusagawa’s Note. The University of Kansas. Archived from the original (PDF) on 2012-03-24. Retrieved 2011-07-10.
  12. ^
    PMID 11848830. Archived from the original
    (PDF) on 2011-08-11. Retrieved 2011-05-16.
  13. ^ .
  14. .
  15. Biochemistry
    (2nd ed.). pp. 295–296.
  16. ^ .
  17. ^ "Aconitase family". The Prosthetic groups and Metal Ions in Protein Active Sites Database Version 2.0. The University of Leeds. 1999-02-02. Archived from the original on 2011-06-08. Retrieved 2011-07-10.

Further reading

External links