Two transcript variants have been identified and this variant (1) represents the longer ACLY transcript. It encodes the longer isoform of ACLY. Placement of code for the initiating methionine, stop codon, poly adenylation signal, boundaries of the 29 exons, and the untranslated region (hatched) are shown. Location of missing sequence in variant 2 compared to variant 1 is indicated in the diagram of the ACLY protein shown below. The sequence for ACLY has been conserved in evolution, putatively from an ancient single gene present prior to separation of animals and fungi with some fungi subsequently developing two genes to code for complete ACLY whereas animals have retained a single gene.

4450 bp mRNA (NCBI RefSeq, May-2012). Multiple Sp1 binding sites and CAAT are present in the promoter of rat ACLY and it can be induced by a low fat/high carbohydrate diet.

None known at this time.

ACLY is a metabolic enzyme found as a tetramer of apparently identical subunits (440000 molecular weight). It was discovered in 1950s. ACLY cleaves citric acid in a multistep process with participation of cofactors to form the products, acetyl-CoA and oxaloacetate. Functional domains of ACLY resemble regions of related enzymes that can play similar roles in metabolism of other substrates.

Four of these subunits form a homotetramer.

Prokaryotes and eukaryotes. The association between increased expression for ACLY and the gene encoding enolase, ENO1, is highly statistically significant. Greater expression of ACLY can be found in mammalian cells under hypoxic conditions. It is more highly expressed in many malignant tissues when compared to their benign counterparts. Aberrant expression can be found in breast, liver, colon, lung, and prostate cancers and is inversely correlated with tumor stage and differentiation so that increased ACLY expression is a negative prognostic factor. ACLYs knockdown in non-small cell lung carcinoma (NSCLC) can lead to apoptosis and differentiation in vitro and less growth in vivo.

ACLY is a relatively abundant cytoplasmic protein and can be associated with outer surfaces of mitochondria and it is also preferentially distributed to pseudopodia in migrating cells. Relatively small amounts have been found in the nuclei. Also, ACLY is found in synaptosomes.

ACLY catalyzes the following reaction: ATP + citrate + CoA = ADP + phosphate + acetyl-CoA + oxaloacetate.
ACLY is well-known for linking carbohydrate and lipid metabolism which can lead to membrane production during cell growth. However, a myriad of other consequences from the breakdown of citrate also occur and are indicated above. Systemically and locally the effects of ACLYs activity can have a powerfull impact. These include alteration of transcription. Citrate passes through nuclear pores and undergoes cleavage by the small amounts of ACLY in the nucleus to generate acetyl CoA that affects transcription via acetylation of histones and transcription factors. Cataplerosis includes citrates transport from the mitochondria via a transporter to provide cytosolic citrate. The transfer of metabolites into mitochondria via shuttles, transporters, etc. constitutes anaplerosis so that either energy or amino acids can be formed, depending on the oxygenation state and the cells needs. Regulation of ACLY is complex and appears to resemble that of glycogen synthase in regard to phosphorylations occurring sequentially in a hierarchical manner. The multiple sources of citrate help to explain the varying effects of ACLY. Note that exogenous citrate can come from anticoagulants. Although ACLY is susceptible to proteolysis, the lower weight (53 kDa) digestion product of ACLY retains its activity.
Loss of ACLY function in plants can result in a bonsai phenotype. Hydroxycitrate, found in the fruit of a tropical tree, Garcinia cambogia (bitter kola) that grows in Southeast Asia and southern India, is a competitive inhibitor and has been extensively used in functional studies. However, solubility issues and the large quantities of hydroxycitrate needed for inhibition of ACLY are disadvantages for using it in clinical studies. Proprietary formulations are available as weight loss supplements and at least one of these has been combined with established anti-cancer agents. The cell-penetrant gamma-lactone, SB-204990, a prodrug of SB-201076, was described in 1998 as an oral drug to inhibit ACLY and has been used in several cancer studies more recently. Radicicol and tartrate are also inhibitors of ACLY. Multiple agents, such as α-lipoic acid, statins, capsaicin, a Met kinase inhibitor (SU11274), etc., have been found to enhance the effects of ACLY inhibitors in small studies of tumors.

ACLY is a member of the acyl-CoA synthetase superfamily (ADP-forming). ACLYs amino terminal region, 1-419, resembles ATP citrate (pro-S)-lyase and the region, 1-424, is homologous to the β-subunit of succinyl-CoA synthetase and the region, 486-818, is homologous to the α-subunit of succinyl-CoA synthetase. Also, the hierarchy of multiple, sequential serine/threonine phosphorylations responsible for the complex regulation of glycogen synthase is similar to the serine/threonine phosphorylations in ACLY. Sequence surrounding the histidine in ACLYs catalytic site, that is phosphorylated by nucleoside diphosphate kinase (NDPK or nm23), is similar to sequence around phosphorylation sites in other substrates of nm23, such as aldolase C. ACLY has homology with citrate synthase that catalyzes its reverse reaction. Rat ACLY is 96,3% identical to human ACLY.

Homozygous knock-out of ACLY in mice is lethal. Heterozygous knock-out mice appear to be normal.