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Last modified: 2 February 1999


Aconitase family

Iron-sulphur cluster Formal oxidation/spin states
Fe4S4 image
[Fe4S4](SgammaCys)3(H2O)n
Active species:

[Fe4S4]+ (S=1/2);
[Fe4S4]2+ (S=0);
[Fe4S4]3+ (S=1/2)

Fe3S4 image
[Fe3S4](SgammaCys)3
Inactive species:

[Fe3S4]0 (S=2);
[Fe3S4]+ (S=1/2)

Aconitase (aconitate hydratase; EC 4.2.1.3) catalyses the stereo­specific isomerisation of citrate to isocitrate via cis­aconitate in the tricarboxylic acid cycle, a non­redox active process [1].

By contrast with the majority of iron-sulphur proteins that function as electron carriers, the Fe-S cluster of aconitase reacts directly with an enzyme substrate [1, 2]. Aconitase has an active [Fe4S4]2+ cluster, which may convert to an inactive [Fe3S4]+ form. Three Cys residues have been shown to be ligands of the [Fe4S4] centre [3]. In the active state, the labile iron ion of the [Fe4S4] cluster is not coordinated by Cys but by water molecules.

The iron­responsive element binding protein (IRE­BP) and 3­isopropylmalate dehydratase (alpha­isopropylmalate isomerase; EC 4.2.1.33), an enzyme catalysing the second step in the biosynthesis of leucine, are known aconitase homologues [4]. Iron regulatory elements (IREs) constitute a family of 28­nucleotide, non­coding, stem­loop structures that regulate iron storage, haem synthesis and iron uptake. They also participate in ribosome binding and control the mRNA turnover (degradation). The specific regulator protein, the IRE­BP, binds to IREs in both 5' and 3' regions [5], but only to RNA in the apo form, without the Fe-S cluster. Expression of IRE­BP in cultured cells has revealed that the protein functions either as an active aconitase, when cells are iron­replete, or as an active RNA­binding protein, when cells are iron­depleted [6]. Mutant IRE­BPs, in which any or all of the three cysteine residues involved in Fe-S formation are replaced by serines, have no aconitase activity, but retain RNA­binding properties [7].

The 3­D structure of mitochondrial aconitase has been determined [2], and has been shown to contain four alpha/ß domains: the three N­terminal domains have similar folds, each with three alphaßalpha layers, while the C­terminal domain forms a ß­barrel (see Figure 7ACN).

Aconitase family proteins in enzyme databases

ENZYME LIGAND BRENDA Official name Alternative name(s)
4.2.1.3
4.2.1.3
4.2.1.3
Aconitate hydratase Aconitase; citrate hydro­lyase
4.2.1.33
4.2.1.33
4.2.1.33
3­Isopropylmalate dehydratase alpha­Isopropylmalate isomerase

Aconitases in motif databases

PRINTS ID PRINTS AC PROSITE/BLOCKS ID PROSITE AC BLOCKS AC
ACONITASE PR00415 ACONITASE PS00450 BL00450

Aconitases in alignment databases

Protein Superfamily Pfam LPFC 3­D alignment
80062; (aconitate hydratase / IREBP)
PF00330; aconitase
-

Aconitases in 3­D databases

All aconitases contain single cubane­like [Fe4S4] cluster except for * (inactive form) containing single [Fe3S4] cluster (see
Figure 7ACN).

PDB scop BSM RELI
Base
Header MMS Abstract ¹
1aco 1aco 1aco 1aco Aconitase (complex with trans­aconitate); bovine heart
-
1ami 1ami 1ami 1ami Aconitase (complex with alpha­methylisocitrate); bovine heart
-
1amj 1amj 1amj 1amj Aconitase (complex with sulphate and hydroxide); bovine heart
-
1b0j 1ar3 1b0j
-
Aconitase (S642A mutant) (complex with isocitrate); pig heart
-
1b0k 1as9 1b0k
-
Aconitase (S642A mutant) (complex with fluorocitrate); pig heart
-
1b0m 1atq 1b0m
-
Aconitase (R644Q mutant) (complex with fluorocitrate); pig heart
-
1fgh 1fgh 1fgh 1fgh Aconitase (complex with 4­hydroxy­trans­aconitate); bovine heart
-
1nis 1nis 1nis 1nis Aconitase (complex with nitrocitrate) (major occupancy form); bovine heart
-
1nit 1nit 1nit 1nit Aconitase (complex with sulphate) (minor occupancy form); bovine heart
-
5acn* 5acn* 5acn* 5acn* Aconitase (inactive [Fe3S4] cluster form) (complex with sulphate and tricarballylic acid); pig heart
-
6acn 6acn 6acn 6acn Aconitase (activated [Fe4S4] cluster form) (complex with sulphate and tricarballylic acid); pig heart
-
7acn 7acn 7acn 7acn Aconitase (complex with isocitrate); pig heart MMS93002
8acn 8acn 8acn 8acn Aconitase (complex with nitroisocitrate); bovine heart MMS93002

¹ Macromolecular Structures abstract. Full text is available to BioMedNet Members

References

  1. Beinert, H. and Kennedy, M.C. (1989) Engineering of protein bound iron-sulfur clusters. A tool for the study of protein and cluster chemistry and mechanism of iron-sulfur enzymes. Eur. J. Biochem. 186, 5-15.
  2. Lauble, H., Kennedy, M.C., Beinert, H. and Stout, C.D. (1994) Crystal structures of aconitase with trans­aconitate and nitrocitrate bound. J. Mol. Biol. 237, 437-451.
  3. Robbins, A.H. and Stout, C.D. (1989) Structure of activated aconitase: formation of the [4Fe-4S] cluster in the crystal. Proc. Natl. Acad. Sci. USA 86, 3639-3643.
  4. Hentze, M.W. and Argos, P. (1991) Homology between IRE­BP, a regulatory RNA­binding protein, aconitase, and isopropylmalate isomerase. Nucleic Acids Res. 19, 1739-1740.
  5. Theil, E.C. (1993) The IRE (iron regulatory element) family: structures which regulate mRNA translation or stability. BioFactors 4, 87-93.
  6. Haile, D.J., Rouault, T.A., Harford, J.B., Kennedy, M.C., Blondin, G.A., Beinert, H. and Klausner, R.D. (1992) Cellular regulation of the iron­responsive element binding protein: disassembly of the cubane iron-sulfur cluster results in high­affinity RNA binding. Proc. Natl. Acad. Sci. USA 89, 11735-11739.
  7. Philpott, C.C., Haile, D.J., Rouault, T.A. and Klausner, R.D. (1993) Modification of a free Fe-S cluster cysteine residue in the active iron­responsive element­binding protein prevents RNA binding. J. Biol. Chem. 268, 17655-17658.
Bibliography on structural studies of aconitase
Reviews on aconitase