F
IPR006249

Aconitase/Iron-responsive element-binding protein 2

InterPro entry
Short nameAconitase/IRP2
Overlapping
homologous
superfamilies
 
family relationships

Description

This entry represents Aconitate hydratase A
[14]
found predominantly in bacteria. Iron-responsive element-binding protein 2
[13]
and Cytoplasmic aconitate hydratase
[12]
from animals; and Aconitate hydratase
[15]
from plants also belong to this family. It also includes Phosphinomethylmalate isomerase (Pmi) involved in the biosynthesis of phosphinothricin tripeptide, a natural-product antibiotic and potent herbicide
[11]
. Pmi has no aconitase activity with citrate as a substrate and is not able to complement an acnA mutant
[11]
.

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
[5, 4]
. 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)
[1]
.


 * 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)
[8, 9]
. 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
[10]
.
 * 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
[6]
. 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
[3]
. 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
[2, 7]
. 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.

References

1.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

2.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

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

4.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

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

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

7.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

8.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

9.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

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

11.The phosphinomethylmalate isomerase gene pmi, encoding an aconitase-like enzyme, is involved in the synthesis of phosphinothricin tripeptide in Streptomyces viridochromogenes. Heinzelmann E, Kienzlen G, Kaspar S, Recktenwald J, Wohlleben W, Schwartz D. Appl Environ Microbiol 67, 3603-9, (2001). View articlePMID: 11472937

12.The bifunctional iron-responsive element binding protein/cytosolic aconitase: the role of active-site residues in ligand binding and regulation. Philpott CC, Klausner RD, Rouault TA. Proc. Natl. Acad. Sci. U.S.A. 91, 7321-5, (1994). View articlePMID: 8041788

13.Molecular characterization of a second iron-responsive element binding protein, iron regulatory protein 2. Structure, function, and post-translational regulation. Samaniego F, Chin J, Iwai K, Rouault TA, Klausner RD. J. Biol. Chem. 269, 30904-10, (1994). PMID: 7983023

14.First Biochemical Characterization of a Methylcitric Acid Cycle from Bacillus subtilis Strain 168. Reddick JJ, Sirkisoon S, Dahal RA, Hardesty G, Hage NE, Booth WT, Quattlebaum AL, Mills SN, Meadows VG, Adams SLH, Doyle JS, Kiel BE. Biochemistry 56, 5698-5711, (2017). View articlePMID: 28956599

15.Selective induction and subcellular distribution of ACONITASE 3 reveal the importance of cytosolic citrate metabolism during lipid mobilization in Arabidopsis. Hooks MA, Allwood JW, Harrison JK, Kopka J, Erban A, Goodacre R, Balk J. Biochem J 463, 309-17, (2014). PMID: 25061985

Cross References

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