| aconitate hydratase |
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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]
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| Identifiers |
| EC number |
4.2.1.3 |
| CAS number |
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 / EGO |
| Search |
| PMC |
articles |
| PubMed |
articles |
| NCBI |
proteins |
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Aconitase family
(aconitate hydratase) |
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Structure of aconitase.[2]
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| Identifiers |
| Symbol |
Aconitase |
| Pfam |
PF00330 |
| InterPro |
IPR001030 |
| PROSITE |
PDOC00423 |
| SCOP |
1aco |
| SUPERFAMILY |
1aco |
| Available protein structures: |
| Pfam |
structures |
| PDB |
RCSB PDB; PDBe; PDBj |
| PDBsum |
structure summary |
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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]
Contents
- 1 Structure
- 2 Function
- 3 Family members
- 4 Interactive pathway map
- 5 References
- 6 Further reading
- 7 External links
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.[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 SO42− 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] 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 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. The iron sulfur cluster is highly sensitive to oxidation by superoxide.[9]
Mechanism
Aconitase arrow-pushing mechanism
[10][11]
Citrate and the Fe-S cluster in the active site of aconitase: dashed yellow lines show interactions between the substrate and nearby residues
[12]
Aconitase employs a dehydration-hydration mechanism.[10] The catalytic residues involved are His-101 and Ser-642.[10] 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, forming a double bond between C2 and C3, forming a cis-aconitate intermediate.[10][13] At this point, the intermediate is rotated 180°.[10] This rotation is referred to as a "flip."[11] Because of this flip, the intermediate is said to move from a "citrate mode" to a "isocitrate mode."[14]
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.[14] This rate-liming step ensures that the right stereochemistry, specifically (2R,3S), is formed in the final product.[14][15] Another hypothesis is that cis-aconitate stays bound to the enzyme while it flips from the citrate to the isocitrate mode.[10]
In either case, flipping cis-aconitate allows the dehydration and hydration steps to occur on opposite faces of the intermediate.[10] Aconitase catalyzes trans elimination/addition of water, and the flip guarantees that the correct stereochemistry is formed in the product.[10][11] 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.[10]
Isocitrate and the Fe-S cluster in the active site of aconitase
[12]PDB: 1C97;
Family members
Aconitases are expressed in bacteria to humans. Humans express the following two aconitase isozymes:
| aconitase 1, soluble |
| Identifiers |
| Symbol |
ACO1 |
| Alt. symbols |
IREB1 |
| Entrez |
48 |
| HUGO |
117 |
| OMIM |
100880 |
| RefSeq |
NM_002197 |
| UniProt |
P21399 |
| Other data |
| EC number |
4.2.1.3 |
| Locus |
Chr. 9 p21.1 |
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| aconitase 2, mitochondrial |
| Identifiers |
| Symbol |
ACO2 |
| Alt. symbols |
ACONM |
| Entrez |
50 |
| HUGO |
118 |
| OMIM |
100850 |
| RefSeq |
NM_001098 |
| UniProt |
Q99798 |
| Other data |
| EC number |
4.2.1.3 |
| Locus |
Chr. 22 q13.2 |
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Interactive pathway map
Click on genes, proteins and metabolites below to link to respective articles. [§ 1]
[[File:
|{{{bSize}}}px|alt=TCA Cycle edit]]
File:TCACycle WP78.png
TCA Cycle edit
- ^ The interactive pathway map can be edited at WikiPathways: "TCACycle_WP78".
References
- ^ PDB: 7ACN; Lauble, H.; Kennedy, M. C.; Beinert, H.; Stout, C. D. (1992). "Crystal structures of aconitase with isocitrate and nitroisocitrate bound". Biochemistry 31 (10): 2735–48. doi:10.1021/bi00125a014. PMID 1547214.
- ^ 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.
- ^ Beinert H, Kennedy MC (Dec 1993). "Aconitase, a two-faced protein: enzyme and iron regulatory factor". FASEB Journal 7 (15): 1442–9. PMID 8262329.
- ^ Flint, Dennis H.; Allen, Ronda M. (1996). "Iron−Sulfur Proteins with Nonredox Functions". Chemical Reviews 96 (7): 2315–34. doi:10.1021/cr950041r.
- ^ 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.
- ^ 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.
- ^ 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. doi:10.1073/pnas.86.10.3639. PMC 287193. PMID 2726740.
- ^ Gardner, Paul R. (2002). "Aconitase: Sensitive target and measure of superoxide". Superoxide Dismutase. Methods in Enzymology 349. pp. 9–23. doi:10.1016/S0076-6879(02)49317-2. ISBN 978-0-12-182252-1.
- ^ a b c d e f g h i Takusagawa F. "Chapter 16: Citric Acid Cycle" (PDF). Takusagawa’s Note. The University of Kansas. Retrieved 2011-07-10.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ "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 8 June 2011. Retrieved 2011-07-10.
Further reading
- Frishman D, Hentze MW (Jul 1996). "Conservation of aconitase residues revealed by multiple sequence analysis. Implications for structure/function relationships". European Journal of Biochemistry / FEBS 239 (1): 197–200. doi:10.1111/j.1432-1033.1996.0197u.x. PMID 8706708.
External links
- Aconitase at the US National Library of Medicine Medical Subject Headings (MeSH)
- Proteopedia Aconitase - the Aconitase structure in interactive 3D
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Metabolism: Citric acid cycle enzymes
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| Cycle |
- Citrate synthase
- Aconitase
- Isocitrate dehydrogenase
- Oxoglutarate dehydrogenase
- Succinyl CoA synthetase
- Succinate dehydrogenase (SDHA)
- Fumarase
- Malate dehydrogenase and ETC
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| Anaplerotic |
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to acetyl-CoA
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- Pyruvate dehydrogenase complex (E1, E2, E3)
- (regulated by Pyruvate dehydrogenase kinase and Pyruvate dehydrogenase phosphatase)
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to α-ketoglutaric acid
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to succinyl-CoA
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to oxaloacetate
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- Pyruvate carboxylase
- Aspartate transaminase
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Mitochondrial
electron transport chain/
oxidative phosphorylation |
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Primary
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- Complex I/NADH dehydrogenase
- Complex II/Succinate dehydrogenase
- Coenzyme Q
- 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
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Other
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- Alternative oxidase
- Electron-transferring-flavoprotein dehydrogenase
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Mitochondrial proteins
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| Outer membrane |
| fatty acid degradation |
- Carnitine palmitoyltransferase I
- Long-chain-fatty-acid—CoA ligase
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| tryptophan metabolism |
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monoamine neurotransmitter
metabolism |
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| Intermembrane space |
- Adenylate kinase
- Creatine kinase
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| Inner membrane |
| oxidative phosphorylation |
- Coenzyme Q – cytochrome c reductase
- Cytochrome c
- NADH dehydrogenase
- Succinate dehydrogenase
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| pyrimidine metabolism |
- Dihydroorotate dehydrogenase
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| mitochondrial shuttle |
- Malate-aspartate shuttle
- Glycerol phosphate shuttle
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| other |
- Glutamate aspartate transporter
- Glycerol-3-phosphate dehydrogenase
- ATP synthase
- Carnitine palmitoyltransferase II
- Uncoupling protein
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| Matrix |
| citric acid cycle |
- Citrate synthase
- Aconitase
- Isocitrate dehydrogenase
- Oxoglutarate dehydrogenase complex
- Succinyl coenzyme A synthetase
- Fumarase
- Malate dehydrogenase
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| anaplerotic reactions |
- Aspartate transaminase
- Glutamate dehydrogenase
- Pyruvate dehydrogenase complex
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| urea cycle |
- Carbamoyl phosphate synthetase I
- Ornithine transcarbamylase
- N-Acetylglutamate synthase
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| alcohol metabolism |
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| Other/to be sorted |
| steroidogenesis |
- Cholesterol side-chain cleavage enzyme
- Steroid 11-beta-hydroxylase
- Aldosterone synthase
- Frataxin
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- Mitochondrial membrane transport protein
- Mitochondrial permeability transition pore
- Mitochondrial carrier
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| Mitochondrial DNA |
| Complex I |
- MT-ND1
- MT-ND2
- MT-ND3
- MT-ND4
- MT-ND4L
- MT-ND5
- MT-ND6
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| Complex III |
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| Complex IV |
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| ATP synthase |
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| 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
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see also mitochondrial diseases
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Carbon-oxygen lyases (EC 4.2) (primarily dehydratases)
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| 4.2.1: Hydro-Lyases |
- Carbonic anhydrase
- Fumarase
- Aconitase
- Enolase
- 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
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| 4.2.2: Acting on polysaccharides |
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| 4.2.3: Acting on phosphates |
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| 4.2.99: Other |
- Carboxymethyloxysuccinate lyase
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Proteins: enzymes
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| Activity |
- Active site
- Binding site
- Catalytic triad
- Oxyanion hole
- Enzyme promiscuity
- Catalytically perfect enzyme
- Coenzyme
- Cofactor
- Enzyme catalysis
- Enzyme kinetics
- Lineweaver–Burk plot
- Michaelis–Menten kinetics
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| Regulation |
- Allosteric regulation
- Cooperativity
- Enzyme inhibitor
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| Classification |
- EC number
- Enzyme superfamily
- Enzyme family
- List of enzymes
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| Types |
- EC1 Oxidoreductases(list)
- EC2 Transferases(list)
- EC3 Hydrolases(list)
- EC4 Lyases(list)
- EC5 Isomerases(list)
- EC6 Ligases(list)
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