G3DSA:3.20.19.10

Aconitase, domain 4

CATH-Gene3D entry
Member databaseCATH-Gene3D
CATH-Gene3D typehomologous superfamily

Description
Imported from IPR015928

Aconitase (aconitate hydratase;
4.2.1.3
) is an iron-sulphur protein that contains a [4Fe-4S]-cluster and catalyses the interconversion of isocitrate and citrate via a cis-aconitate intermediate. Aconitase functions in both the TCA and glyoxylate cycles, however unlike the majority of iron-sulphur proteins that function as electron carriers, the [4Fe-4S]-cluster of aconitase reacts directly with an enzyme substrate. In eukaryotes there is a cytosolic form (cAcn) and a mitochondrial form (mAcn) of the enzyme. In bacteria there are also 2 forms, aconitase A (AcnA) and B (AcnB). Several aconitases are known to be multi-functional enzymes with a second non-catalytic, but essential function that arises when the cellular environment changes, such as when iron levels drop
[9, 7]
. Eukaryotic cAcn and mAcn, and bacterial AcnA have the same domain organisation, consisting of three N-terminal α/β/α domains, a linker region, followed by a C-terminal 'swivel' domain with a β/β/α structure (1-2-3-linker-4), although mAcn is smaller than cAcn. However, bacterial AcnB has a different organisation: it contains an N-terminal HEAT-like domain, followed by the 'swivel' domain, then the three α/β/α domains (HEAT-4-1-2-3)
[2]
.


 * Eukaryotic cAcn enzyme balances the amount of citrate and isocitrate in the cytoplasm, which in turn creates a balance between the amount of NADPH generated from isocitrate by isocitrate dehydrogenase with the amount of acetyl-CoA generated from citrate by citrate lyase. Fatty acid synthesis requires both NADPH and acetyl-CoA, as do other metabolic processes, including the need for NADPH to combat oxidative stress. The enzymatic form of cAcn predominates when iron levels are normal, but if they drop sufficiently to cause the disassembly of the [4Fe-4S]-cluster, then cAcn undergoes a conformational change from a compact enzyme to a more open L-shaped protein known as iron regulatory protein 1 (IRP1; or IRE-binding protein 1, IREBP1)
[12, 13]
. As IRP1, the catalytic site and the [4Fe-4S]-cluster are lost, and two new RNA-binding sites appear. IRP1 functions in the post-transcriptional regulation of genes involved in iron metabolism -it binds to mRNA iron-responsive elements (IRE), 30-nucleotide stem-loop structures at the 3' or 5' end of specific transcripts. Transcripts containing an IRE include ferritin L and H subunits (iron storage), transferrin (iron plasma chaperone), transferrin receptor (iron uptake into cells), ferroportin (iron exporter), mAcn, succinate dehydrogenase, erythroid aminolevulinic acid synthetase (tetrapyrrole biosynthesis), among others. If the IRE is in the 5'-UTR of the transcript (e.g. in ferritin mRNA), then IRP1-binding prevents its translation by blocking the transcript from binding to the ribosome. If the IRE is in the 3'-UTR of the transcript (e.g. transferrin receptor), then IRP1-binding protects it from endonuclease degradation, thereby prolonging the half-life of the transcript and enabling it to be translated
[14]
.
 * IRP2 is another IRE-binding protein that binds to the same transcripts as IRP1. However, since IRP1 is predominantly in the enzymatic cAcn form, it is IRP2 that acts as the major metabolic regulator that maintains iron homeostasis
[10]
. Although IRP2 is homologous to IRP1, IRP2 lacks aconitase activity, and is known only to have a single function in the post-transcriptional regulation of iron metabolism genes
[6]
. In iron-replete cells, IRP2 activity is regulated primarily by iron-dependent degradation through the ubiquitin-proteasomal system.
 * Bacterial AcnB is also known to be multi-functional. In addition to its role in the TCA cycle, AcnB was shown to be a post-transcriptional regulator of gene expression in Escherichia coli and Salmonella enterica
[5, 11]
. In S. enterica, AcnB initiates a regulatory cascade controlling flagella biosynthesis through an interaction with the ftsH transcript, an alternative RNA polymerase sigma factor. This binding lowers the intracellular concentration of FtsH protease, which in turn enhances the amount of RNA polymerase sigma32 factor (normally degraded by FtsH protease), and sigma32 then increases the synthesis of chaperone DnaK, which in turn promotes the synthesis of the flagellar protein FliC. AcnB regulates the synthesis of other proteins as well, such as superoxide dismutase (SodA) and other enzymes involved in oxidative stress.


3-isopropylmalate dehydratase (or isopropylmalate isomerase;
4.2.1.33
) catalyses the stereo-specific isomerisation of 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. This enzyme performs the second step in the biosynthesis of leucine, and is present in most prokaryotes and many fungal species. The prokaryotic enzyme is a heterodimer composed of a large (LeuC) and small (LeuD) subunit, while the fungal form is a monomeric enzyme. Both forms of isopropylmalate are related and are part of the larger aconitase family
[2]
. Aconitases are mostly monomeric proteins which share four domains in common and contain a single, labile [4Fe-4S] cluster. Three structural domains (1, 2 and 3) are tightly packed around the iron-sulphur cluster, while a fourth domain (4) forms a deep active-site cleft. The prokaryotic enzyme is encoded by two adjacent genes, leuC and leuD, corresponding to aconitase domains 1-3 and 4 respectively
[4, 3]
. LeuC does not bind an iron-sulphur cluster. It is thought that some prokaryotic isopropylamalate dehydrogenases can also function as homoaconitase
4.2.1.36
, converting cis-homoaconitate to homoisocitric acid in lysine biosynthesis
[8]
. Homoaconitase has been identified in higher fungi (mitochondria) and several archaea and one thermophilic species of bacteria, Thermus thermophilus
[15]
. It is also found in the higher plant Arabidopsis thaliana, where it is targeted to the chloroplast
[1]
.

This superfamily represents the 'swivel' domain found at the C-terminal of eukaryotic mAcn, cAcn/IPR1 and IRP2, and bacterial AcnA, but in the N-terminal region following the HEAT-like domain in bacterial AcnB. This domain has a three layer β/β/α structure, and in cytosolic Acn is known to rotate between the cAcn and IRP1 forms of the enzyme. This domain is also found in the small subunit of isopropylmalate dehydratase (LeuD).

References
Imported from IPR015928

1.Functional specification of Arabidopsis isopropylmalate isomerases in glucosinolate and leucine biosynthesis. He Y, Chen B, Pang Q, Strul JM, Chen S. Plant Cell Physiol. 51, 1480-7, (2010). View articlePMID: 20663849

2.The aconitase family: three structural variations on a common theme. Gruer MJ, Artymiuk PJ, Guest JR. Trends Biochem. Sci. 22, 3-6, (1997). View articlePMID: 9020582

3.The organization of the leuC, leuD and leuB genes of the extreme thermophile Thermus thermophilus. Tamakoshi M, Yamagishi A, Oshima T. Gene 222, 125-32, (1998). View articlePMID: 9813279

4.Branched-chain amino acid biosynthesis genes in Lactococcus lactis subsp. lactis. Godon JJ, Chopin MC, Ehrlich SD. J. Bacteriol. 174, 6580-9, (1992). View articlePMID: 1400210

5.Switching aconitase B between catalytic and regulatory modes involves iron-dependent dimer formation. Tang Y, Guest JR, Artymiuk PJ, Green J. Mol. Microbiol. 56, 1149-58, (2005). View articlePMID: 15882410

6.Evolution of the iron-responsive element. Piccinelli P, Samuelsson T. RNA 13, 952-66, (2007). View articlePMID: 17513696

7.Single-gene disorders: what role could moonlighting enzymes play? Sriram G, Martinez JA, McCabe ER, Liao JC, Dipple KM. Am. J. Hum. Genet. 76, 911-24, (2005). View articlePMID: 15877277

8.Crystal structure of the Pyrococcus horikoshii isopropylmalate isomerase small subunit provides insight into the dual substrate specificity of the enzyme. Yasutake Y, Yao M, Sakai N, Kirita T, Tanaka I. J. Mol. Biol. 344, 325-33, (2004). View articlePMID: 15522288

9.Moonlighting proteins. Jeffery CJ. Trends Biochem. Sci. 24, 8-11, (1999). View articlePMID: 10087914

10.The role of iron regulatory proteins in mammalian iron homeostasis and disease. Rouault TA. Nat. Chem. Biol. 2, 406-14, (2006). View articlePMID: 16850017

11.Post-transcriptional regulation of bacterial motility by aconitase proteins. Tang Y, Guest JR, Artymiuk PJ, Read RC, Green J. Mol. Microbiol. 51, 1817-26, (2004). View articlePMID: 15009904

12.Structure of dual function iron regulatory protein 1 complexed with ferritin IRE-RNA. Walden WE, Selezneva AI, Dupuy J, Volbeda A, Fontecilla-Camps JC, Theil EC, Volz K. Science 314, 1903-8, (2006). View articlePMID: 17185597

13.Crystal structure of human iron regulatory protein 1 as cytosolic aconitase. Dupuy J, Volbeda A, Carpentier P, Darnault C, Moulis JM, Fontecilla-Camps JC. Structure 14, 129-39, (2006). View articlePMID: 16407072

14.Cell biology. "Pumping" iron: the proteins. Beutler E. Science 306, 2051-3, (2004). View articlePMID: 15604397

15.Kinetics and product analysis of the reaction catalysed by recombinant homoaconitase from Thermus thermophilus. Jia Y, Tomita T, Yamauchi K, Nishiyama M, Palmer DR. Biochem. J. 396, 479-85, (2006). View articlePMID: 16524361

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