The Acetyl-CoA Carboxylase (ACC) Project
Updated Jan. 2018
Acetyl-CoA carboxylase (ACC) catalyzes the biotin-dependent carboxylation
of acetyl-CoA to produce malonyl-CoA. This is the first and the committed
step in the biosynthesis of long-chain fatty acids. At the same time, a
second isoform of ACC, ACC2, is associated with the mitochondrial membrane
and produces malonyl-CoA that regulates fatty acid oxidation by potently
inhibiting the carnitine palmitoyltransferases (CPT-Is).
Mice that are
deficient in ACC2 have elevated fatty acid oxidation and
reduced body fat content and body weight, despite consuming more food.
Therefore, inhibitors against ACCs might be efficacious for the
treatment of obesity and diabetes (metabolic syndrome).
ACCs are multi-subunit enzymes in prokaryotes, whereas most eukaryotic
ACCs are multi-domain enzymes. The biotin carboxylase (BC) domain
catalyzes the first step of the reaction: the carboxylation of the
biotin prosthetic group that is covalently linked to the biotin
carboxyl carrier protein (BCCP) domain. In the second step of the
reaction, the carboxyltransferase (CT) domain catalyzes the
transfer of the carboxyl group from (carboxy)biotin to acetyl-CoA.
Some commercial herbicides (exemplified by haloxyfop, tepraloxydim,
kill plants by inhibiting the CT domain of
their plastid ACC and thereby shutting down
fatty acid biosynthesis. More recently, CP-640186 has been reported
by Pfizer as a potent inhibitor of both isoforms of mammalian ACCs.
Other potent inhibitors of mammalian ACCs have also been reported,
some with significant selectivity between the two isoforms.
Soraphen A, a macrocyclic polyketide natural product, is a
nanomolar inhibitor of the BC domain of eukaryotic ACCs, but it
has no activity against the bacterial BC subunits.
While structures of the E. coli BC and BCCP subunits had been
reported, no structural information was available for
the CT domain. The CT domain shares no recognizable amino acid
sequence homology to other proteins in the database.
Major findings from this project
- The crystal structure of the CT domain of yeast ACC has been
determined at 2.7A resolution.
- The structure contains two domains, which share the same backbone
folds. This fold belongs to the crotonase/ClpP family of proteins,
with a b-b-a superhelix.
- There are many insertions on the surface of the domain, which
are important for the dimerization of this enzyme.
- The domain exists as dimers in solution, with the monomers
arranged in a head-to-tail fashion.
- The active site of the enzyme is located at the dimer inteface.
We have determined the binding mode of CoA to the enzyme.
- Commercial herbicides inhibit CT at the active site.
- The structure of the haloxyfop herbicide in complex with the
CT domain has been determined at 2.7A resolution.
- Haloxyfop is bound near the active site, but its binding
large conformational changes for several residues in the active
- Two residues that confer resistance to the herbicides when
mutated in plant ACCs, equivalent to Leu1705 and Val1967 of
yeast ACC, are in the haloxyfop binding site.
- The structure of the tepraloxydim herbicide in complex with the
CT domain has been determined at 2.3A resolution.
- Tepraloxydim interacts with a different region of the dimer interface
as compared to haloxyfop, and requires only a small conformational change
in CT for binding.
- The structure of the pinoxaden herbicide in complex with the
CT domain has been determined at 2.8A resolution.
- Pinoxaden is also located in the dimer interface region,
and requires a small conformational change in CT for binding.
- The three herbicides do share two anchoring interactions with CT.
An oxyanion that is recognized by two main-chain amides of CT, and a
small aliphatic group (methyl or ethyl) that is located in a small
hydrophobic pocket (lined by Leu1705 among other side chains).
These interactions may provide an important
lead for developing new CT inhibitors.
- The structure of yeast CT in complex with CP-640186 has
been determined at 2.7A resolution.
- CP-640186 is bound in the putative biotin binding site
of CT, and causes only minor conformational change in the
- The compounds CoA, haloxyfop, and CP-640186 identify
three distinct regions in the active site of CT that could
be used for developing inhibitors.
- The structure of yeast BC in complex with soraphen A
has been determined at 1.8A resolution.
- Soraphen A may inhibit BC with a novel mechanism, by
inhibiting its dimerization.
- The binding site for soraphen A is unique to the
eukaryotic BC domains, thereby explaining its specificity.
- Dimerization of the E. coli BC subunit was believed
to be required for its activity. We have generated mutants
in the dimer interface that remain monomeric at micromolar
concentrations. These mutants are active catalytically,
suggesting that dimerization is not absolutely required
- Soraphen A may stabilize a form of the BC domain that is
incompatible with catalysis.
- The structure of wild-type E. coli BC in complex with Mg-ADP, biotin
and bicarbonate has been determined at 2A resolution. The BC dimer
is fully symmetrical in this substrate complex.
- Glu296 is the general base for the BC reaction, and Arg338
helps to stabilize the enolate biotin intermediate.
- The crystal structure of the 500kD, full-length yeast ACC holoenzyme dimer has been
- The unique, central region of eukaryotic ACC contains five domains, and forms a
scaffold to position the BC and CT domains for catalysis. This region has no direct
contributions to either active site.
- BC is a dimer in the holoenzyme, in contrast to the structure of the BC domain alone.
- There are large conformational changes in the BC dimer interface, as well as near the
biotin binding site in the BC active site.
- The structure suggests the molecular mechanism for the inhibition of BC catalysis by
soraphen A as well as by phosphorylation of a Ser residue just prior to the BC domain core.
Both stabilize a conformation of the BC domain that is catalytically inactive (due to
blocking of biotin binding) and incompatible with dimerization (due to the conformational
change in the dimer interface).
- Potent small-molecule inhibitors of human ACCs have been
developed using the soraphen A binding site.
ND-630 is currently in clinical trials against liver disease.
- The phosphorylation site in yeast ACC by the AMPK homolog SNF1 has been confirmed as Ser1157.
- Phosphorylation of Ser1157 inhibits the activity of yeast ACC.
- pSer1157 is recognized by Arg1173 and Arg1260, and other residues. The R1173A/R1260A double
mutation abolishes the inhibition by SNF1.
- Phosphorylation of Ser1157 stabilizes a conformation of the central region of yeast ACC that
is incompatible with BC domain dimerization and catalysis.
- Ser1157 phosphorylated yeast ACC assumes a mostly elongated conformation, with disrupted BC domain dimers, similar to the observation in the presence of soraphen A.
- Phosphorylation just prior to the BC domain of ACC (and soraphen A binding) and near the
central region of ACC share a unified mechanism of inhibiting ACC, by stabilizing a conformation
that is incompatible with BC domain dimerization.
Publications from this project
H. Zhang, Z. Yang, Y. Shen & L. Tong. (2003).
Crystal structure of the carboxyltransferase domain of acetyl-coenzyme A
Science, 299, 2064-2067.
H. Zhang, B. Tweel & L. Tong. (2004).
Molecular basis for the inhibition of the carboxyltransferase
domain of acetyl-coenzyme A carboxylase by haloxyfop and diclofop.
Proc. Natl. Acad. Sci. USA, 101, 5910-5915.
H. Zhang, B. Tweel, J. Li & L. Tong. (2004).
Crystal structure of the carboxyltransferase domain
of acetyl-coenzyme A carboxylase in complex with
Structure, 12, 1683-1691.
Y. Shen, S.L. Volrath, S.C. Weatherly, T.D. Elich &
L. Tong. (2004).
A mechanism for the potent inhibition of eukaryotic
acetyl coenzyme A carboxylase by soraphen A, a macrocyclic
polyketide natural product.
Mol. Cell, 16, 881-891.
L. Tong. (2005).
Acetyl-coenzyme A carboxylase: crucial metabolic enzyme
and attractive target for drug discovery.
Cell. Mol. Life Sci., 62, 1784-1803.
Y. Shen, C.-Y. Chou, G.-G. Chang &
L. Tong. (2006).
Is dimerization required for the catalytic activity
of bacterial biotin carboxylase?
Mol. Cell, 22, 807-818.
L. Tong & H.J. Harwood, Jr. (2006).
Acetyl-coenzyme A carboxylases: versatile targets for drug discovery.
J. Cell. Biochem., 99, 1476-1488.
Y. Shen & L. Tong. (2008).
Structural evidence for direct interactions between the BRCT domains of human BRCA1 and a
phospho-peptide from human ACC1.
Biochem., 47, 5767-5773.
C.-Y. Chou, L.P.C. Yu & L. Tong. (2009).
Crystal structure of biotin carboxylase in complex with substrates
and implications for its catalytic mechanism.
J. Biol. Chem., 284, 11690-11697.
S. Xiang, M.M. Callaghan, K.G. Watson & L. Tong. (2009).
A different mechanism for the inhibition of the
carboxyltransferase domain of acetyl-coenzyme A carboxylase by tepraloxydim.
Proc. Natl. Acad. Sci. USA, 106, 20723-20727.
L.P.C. Yu, Y.S. Kim & L. Tong. (2010). Mechanism for the inhibition
of the carboxyltransferase domain of acetyl-coenzyme A carboxylase by pinoxaden.
Proc. Natl. Acad. Sci. USA, 107, 22072-22077.
C.-Y. Chou & L. Tong. (2011). Structural and biochemical studies on the regulation
of biotin carboxylase by substrate inhibition and dimerization.
J. Biol. Chem., 286, 24417-24425.
C. Fan, C.-Y. Chou, L. Tong & S. Xiang. (2012).
Crystal structure of urea carboxylase provides insights into the
carboxyltransfer reaction. J. Biol. Chem. 287, 9389-9398.
L. Tong. (2013).
Structure and function of biotin-dependent carboxylases.
Cell. Mol. Life Sci. 70, 863-891.
T.H. Tran, Y.-S. Hsiao, J. Jo, C.-Y. Chou, L.E. Dietrich, T. Walz & L. Tong. (2015).
Structure and function of a single-chain, multi-domain long-chain acyl-CoA carboxylase.
Nature, 518, 120-124.
J. Wei & L. Tong. (2015).
Crystal structure of the 500-kDa yeast acetyl-CoA carboxylase
Nature, 526, 723-727.
G. Harriman, J. Greenwood, S. Bhat, X. Huang, R. Wang, D. Paul,
L. Tong, A.K. Saha, W.F. Westlin, R. Kapeller & H.J. Harwood Jr. (2016).
Acetyl-CoA carboxylase inhibition by ND-630 reduces hepatic
steatosis, improves insulin sensitivity, and modulates dyslipidemia
Proc. Natl. Acad. Sci. USA, 113, E1796-E1805.
J. Wei, Y. Zhang, T.-Y. Yu, K. Sadre-Bazzaz, M.J. Rudolph,
G.A. Amodeo, L.S. Symington, T. Walz & L. Tong. (2016).
A unified molecular mechanism for the regulation of acetyl-CoA
carboxylase by phosphorylation.
Cell Discovery, 2, 16044.
Funding for this project
© copyright 2003-2018, Liang Tong.