Aconitase

Class of enzymes

aconitate hydratase

Illustration of pig aconitase in complex with the [Fe4S4] cluster. The protein is colored by secondary structure, and iron atoms are blue and the sulfur red.[1]

Identifiers
EC no.| 4.2.1.3
CAS no.| 9024-25-3
Databases
IntEnz| IntEnz view
BRENDA| BRENDA entry
ExPASy| NiceZyme view
KEGG| KEGG entry
MetaCyc| metabolic pathway
PRIAM| profile
PDB structures| RCSB PDB PDBe PDBsum
Gene Ontology| AmiGO  / QuickGO
| Search

PMC| articles
PubMed| articles
NCBI| proteins

Protein family

Aconitase family
(aconitate hydratase)

Structure of aconitase.[2]

Identifiers
Symbol| Aconitase
Pfam| PF00330
InterPro| IPR001030
PROSITE| PDOC00423
SCOP2| 1aco / SCOPe / SUPFAM
| Available protein structures:

Pfam | structures / ECOD
PDB| RCSB PDB; PDBe; PDBj
PDBsum| structure summary

Aconitase (aconitate hydratase; EC 4.2.1.3) is an enzyme that catalyses the stereo-specific isomerization of citrate to isocitrate via cis-aconitate in the tricarboxylic acid cycle, a non-redox-active process.[3][4][5]

* Citric acid

* Aconitic acid

* Isocitric acid

## Structure

[edit]

Aconitase has two slightly different structures, depending on whether it is activated or inactivated.[6][7] In the inactive form, its structure is divided into four domains.[6] Counting from the N-terminus, only the first three of these domains are involved in close interactions with the [3Fe-4S] cluster, but the active site consists of residues from all four domains, including the larger 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

[edit]

In contrast with the majority of iron-sulfur proteins that function as electron carriers, the 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 iron-responsive element-binding protein (IRE-BP) and 3-isopropylmalate dehydratase (α-isopropylmalate isomerase; EC 4.2.1.33), an enzyme catalysing the second step in the biosynthesis of leucine, are known aconitase homologues. Iron regulatory elements (IREs) constitute a family of 28-nucleotide, non-coding, stem-loop structures that regulate iron storage, heme synthesis and iron uptake. They also participate in ribosome binding and control 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

[edit]

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.[11] The catalytic residues involved are His-101 and Ser-642.[11] His-101 protonates the hydroxyl group on C3 of citrate, allowing it to leave as water, and Ser-642 concurrently abstracts the proton on C2, creating a double bond between C2 and C3, and forming the so-called cis-aconitate intermediate (the two carboxyl groups on the double bond are cis).[11][14] The carbon atom from which the hydrogen is removed is the one that came from oxaloacetate in the previous step of the citric acid cycle, not the one that came from 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

[edit]

Aconitases are expressed in bacteria to humans. In citrus fruits, a reduction of the activity of the mitochondrial aconitases likely leads to the buildup of citric acid, which is then stored in vacuoles.[18] As the fruit matures, citric acid is returned back to the cytosol where an increase in cytosolic aconitase activity reduces its levels in the fruit.[18] Humans express the following two aconitase isozymes:

| aconitase 1, soluble

Identifiers
Symbol| ACO1
Alt. symbols| IREB1
NCBI gene| 48
HGNC| 117
OMIM| 100880
RefSeq| NM_002197
UniProt| P21399
Other data
EC number| 4.2.1.3
Locus| Chr. 9 p21.1
| Search for

Structures| Swiss-model
Domains| InterPro
| aconitase 2, mitochondrial

Identifiers
Symbol| ACO2
Alt. symbols| ACONM
NCBI gene| 50
HGNC| 118
OMIM| 100850
RefSeq| NM_001098
UniProt| Q99798
Other data
EC number| 4.2.1.3
Locus| Chr. 22 q13.2
| Search for

Structures| Swiss-model
Domains| InterPro

## Interactive pathway map

[edit]

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

[[File:

|alt=TCACycle_WP78 edit]]

TCACycle_WP78 edit

1. ^ The interactive pathway map can be edited at WikiPathways: "TCACycle_WP78".

## References

[edit]

1. ^ PDB: 7ACN​; Lauble H, Kennedy MC, Beinert H, Stout CD (1992). "Crystal structures of aconitase with isocitrate and nitroisocitrate bound". Biochemistry. 31 (10): 2735–48\. doi:10.1021/bi00125a014. PMID 1547214.
2. ^ PDB: 1ACO​; Lauble H, Kennedy MC, Beinert H, Stout CD (1994). "Crystal Structures of Aconitase with Trans-aconitate and Nitrocitrate Bound". Journal of Molecular Biology. 237 (4): 437–51\. doi:10.1006/jmbi.1994.1246. PMID 8151704.
3. ^ Beinert H, Kennedy MC (Dec 1993). "Aconitase, a two-faced protein: enzyme and iron regulatory factor". FASEB Journal. 7 (15): 1442–9\. doi:10.1096/fasebj.7.15.8262329. PMID 8262329. S2CID 1107246.
4. ^ Flint DH, Allen RM (1996). "Iron−Sulfur Proteins with Nonredox Functions". Chemical Reviews. 96 (7): 2315–34\. doi:10.1021/cr950041r. PMID 11848829.
5. ^ Beinert H, Kennedy MC, Stout CD (Nov 1996). "Aconitase as Ironminus signSulfur Protein, Enzyme, and Iron-Regulatory Protein". Chemical Reviews. 96 (7): 2335–2374\. doi:10.1021/cr950040z. PMID 11848830.
6. ^ a b c d Robbins AH, Stout CD (1989). "The structure of aconitase". Proteins. 5 (4): 289–312\. doi:10.1002/prot.340050406. PMID 2798408. S2CID 36219029.
7. ^ a b c Robbins AH, Stout CD (May 1989). "Structure of activated aconitase: formation of the [4Fe-4S] cluster in the crystal". Proceedings of the National Academy of Sciences of the United States of America. 86 (10): 3639–43\. Bibcode:1989PNAS...86.3639R. doi:10.1073/pnas.86.10.3639. PMC 287193. PMID 2726740.
8. ^ Lauble H, Kennedy MC, Beinert H, Stout CD (Mar 1992). "Crystal structures of aconitase with isocitrate and nitroisocitrate bound". Biochemistry. 31 (10): 2735–48\. doi:10.1021/bi00125a014. PMID 1547214.
9. ^ Morrison JF, Peters RA (November 1954). "Biochemistry of fluoroacetate poisoning: the effect of fluorocitrate on purified aconitase". Biochem. J. 58 (3): 473–9\. doi:10.1042/bj0580473. PMC 1269923. PMID 13208639.
10. ^ Gardner PR (2002). "Aconitase: Sensitive target and measure of superoxide". Superoxide Dismutase. Methods in Enzymology. Vol. 349\. pp. 9–23\. doi:10.1016/S0076-6879(02)49317-2. ISBN 978-0-12-182252-1. PMID 11912933.
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. ^ a b c Beinert H, Kennedy MC, Stout CD (Nov 1996). "Aconitase as Ironminus signSulfur Protein, Enzyme, and Iron-Regulatory Protein" (PDF). Chemical Reviews. 96 (7): 2335–2374\. doi:10.1021/cr950040z. PMID 11848830. Archived from the original (PDF) on 2011-08-11. Retrieved 2011-05-16.
13. ^ a b PDB: 1C96​; Lloyd SJ, Lauble H, Prasad GS, Stout CD (December 1999). "The mechanism of aconitase: 1.8 A resolution crystal structure of the S642a:citrate complex". Protein Sci. 8 (12): 2655–62\. doi:10.1110/ps.8.12.2655. PMC 2144235. PMID 10631981.
14. ^ Han D, Canali R, Garcia J, Aguilera R, Gallaher TK, Cadenas E (Sep 2005). "Sites and mechanisms of aconitase inactivation by peroxynitrite: modulation by citrate and glutathione". Biochemistry. 44 (36): 11986–96\. doi:10.1021/bi0509393. PMID 16142896.
15. ^ Lubert Stryer (1981). Biochemistry (2nd ed.). pp. 295–296.
16. ^ a b c Lauble H, Stout CD (May 1995). "Steric and conformational features of the aconitase mechanism". Proteins. 22 (1): 1–11\. doi:10.1002/prot.340220102. PMID 7675781. S2CID 43006515.
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.
18. ^ a b Degu A, Hatew B, Nunes-Nesi A, Shlizerman L, Zur N, Katz E, Fernie AR, Blumwald E, Sadka A (September 2011). "Inhibition of aconitase in citrus fruit callus results in a metabolic shift towards amino acid biosynthesis". Planta. 234 (3): 501–513\. doi:10.1007/s00425-011-1411-2.

## Further reading

[edit]

* Frishman D, Hentze MW (Jul 1996). "Conservation of aconitase residues revealed by multiple sequence analysis. Implications for structure/function relationships". European Journal of Biochemistry. 239 (1): 197–200\. doi:10.1111/j.1432-1033.1996.0197u.x. PMID 8706708.

## External links

[edit]

* Aconitase at the U.S. National Library of Medicine Medical Subject Headings (MeSH)
* Proteopedia Aconitase \- the Aconitase structure in interactive 3D

* v
* t
* e

Metabolism: Citric acid cycle enzymes

Cycle|

* Citrate synthase
* Aconitase
* Isocitrate dehydrogenase
* Oxoglutarate dehydrogenase
* Succinyl CoA synthetase

* Succinate dehydrogenase (SDHA)
* Fumarase
* Malate dehydrogenase and ETC

Anaplerotic|

| to acetyl-CoA|

* Pyruvate dehydrogenase complex (E1, E2, E3)

* (regulated by Pyruvate dehydrogenase kinase and Pyruvate dehydrogenase phosphatase)

|

to α-ketoglutaric acid|

* Glutamate dehydrogenase

to succinyl-CoA|

* Methylmalonyl-CoA mutase

to oxaloacetic acid|

* Pyruvate carboxylase
* Aspartate transaminase

Mitochondrial
electron transport chain/
oxidative phosphorylation|

| Primary|

* Complex I/NADH dehydrogenase
* Complex II/Succinate dehydrogenase
* Coenzyme Q10 (CoQ10)
* Complex III/Coenzyme Q - cytochrome c reductase
* Cytochrome c
* Complex IV/Cytochrome c oxidase

* Coenzyme Q10 synthesis: COQ2
* COQ3
* COQ4
* COQ5
* COQ6
* COQ7
* COQ9
* COQ10A
* COQ10B
* PDSS1
* PDSS2

|

Other|

* Alternative oxidase
* Electron-transferring-flavoprotein dehydrogenase

* v
* t
* e

Mitochondrial proteins

Outer membrane|

| fatty acid degradation|

* Carnitine palmitoyltransferase I
* Long-chain-fatty-acid—CoA ligase

|

tryptophan metabolism|

* Kynureninase

monoamine neurotransmitter
metabolism|

* Monoamine oxidase

Intermembrane space|

* Adenylate kinase
* Creatine kinase

Inner membrane|

| oxidative phosphorylation|

* Coenzyme Q – cytochrome c reductase
* Cytochrome c
* NADH dehydrogenase
* Succinate dehydrogenase

|

pyrimidine metabolism|

* Dihydroorotate dehydrogenase

mitochondrial shuttle|

* Malate-aspartate shuttle
* Glycerol phosphate shuttle

steroidogenesis|

* Cholesterol side-chain cleavage enzyme
* Steroid 11-beta-hydroxylase
* Aldosterone synthase

other|

* Glutamate aspartate transporter
* Glycerol-3-phosphate dehydrogenase
* ATP synthase
* Carnitine palmitoyltransferase II
* Uncoupling protein

Matrix|

| citric acid cycle|

* Citrate synthase
* Aconitase
* Isocitrate dehydrogenase
* Oxoglutarate dehydrogenase complex
* Succinyl coenzyme A synthetase
* Fumarase
* Malate dehydrogenase

|

anaplerotic reactions|

* Aspartate transaminase
* Glutamate dehydrogenase
* Pyruvate dehydrogenase complex

urea cycle|

* Carbamoyl phosphate synthetase I
* Ornithine transcarbamylase
* N-Acetylglutamate synthase

alcohol metabolism|

* ALDH2

* PMPCB

Other/to be sorted|

* Frataxin
* Mitochondrial membrane transport protein
* Mitochondrial permeability transition pore
* Mitochondrial carrier
* Translocator protein

Mitochondrial DNA|

| Complex I|

* MT-ND1
* MT-ND2
* MT-ND3
* MT-ND4
* MT-ND4L
* MT-ND5
* MT-ND6

|

Complex III|

* MT-CYB

Complex IV|

* MT-CO1
* MT-CO2
* MT-CO3

ATP synthase|

* MT-ATP6
* MT-ATP8

tRNA|

* MT-TA
* MT-TC
* MT-TD
* MT-TE
* MT-TF
* MT-TG
* MT-TH
* MT-TI
* MT-TK
* MT-TL1
* MT-TL2
* MT-TM
* MT-TN
* MT-TP
* MT-TQ
* MT-TR
* MT-TS1
* MT-TS2
* MT-TT
* MT-TV
* MT-TW
* MT-TY

see also mitochondrial diseases

* v
* t
* e

Carbon–oxygen lyases (EC 4.2) (primarily dehydratases)

4.2.1: Hydro-Lyases|

* Carbonic anhydrase
* Fumarase
* Aconitase
* Enolase
* Alpha
* Enolase 2
* Enoyl-CoA hydratase/3-Hydroxyacyl ACP dehydrase
* Methylglutaconyl-CoA hydratase
* Tryptophan synthase
* Cystathionine beta synthase
* Porphobilinogen synthase
* 3-Isopropylmalate dehydratase
* Urocanase
* Uroporphyrinogen III synthase
* Nitrile hydratase

4.2.2: Acting on polysaccharides|

* Hyaluronate lyase
* Pectin lyase

4.2.3: Acting on phosphates|

* Threonine synthase

4.2.99: Other|

* Carboxymethyloxysuccinate lyase
* Hydroperoxide lyase

* v
* t
* e

Enzymes

Activity|

* Active site
* Binding site
* Catalytic triad
* Oxyanion hole
* Enzyme promiscuity
* Diffusion-limited enzyme
* Cofactor
* Enzyme catalysis

Regulation|

* Allosteric regulation
* Cooperativity
* Enzyme inhibitor
* Enzyme activator

Classification|

* EC number
* Enzyme superfamily
* Enzyme family
* List of enzymes

Kinetics|

* Enzyme kinetics
* Eadie–Hofstee diagram
* Hanes–Woolf plot
* Lineweaver–Burk plot
* Michaelis–Menten kinetics

Types|

* EC1 Oxidoreductases (list)
* EC2 Transferases (list)
* EC3 Hydrolases (list)
* EC4 Lyases (list)
* EC5 Isomerases (list)
* EC6 Ligases (list)
* EC7 Translocases (list)

Portal:

* Biology

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