Polyketide Synthase
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Polyketide synthases (PKSs) are a family of multi- domain
enzyme An enzyme () is a protein that acts as a biological catalyst by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates into different mol ...
s or enzyme complexes that produce
polyketide In organic chemistry, polyketides are a class of natural products derived from a Precursor (chemistry), precursor molecule consisting of a Polymer backbone, chain of alternating ketone (, or Carbonyl reduction, its reduced forms) and Methylene gro ...
s, a large class of
secondary metabolites Secondary metabolites, also called ''specialised metabolites'', ''secondary products'', or ''natural products'', are organic compounds produced by any lifeform, e.g. bacteria, archaea, fungi, animals, or plants, which are not directly involved ...
, in
bacteria Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...
,
fungi A fungus (: fungi , , , or ; or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and mold (fungus), molds, as well as the more familiar mushrooms. These organisms are classified as one ...
,
plant Plants are the eukaryotes that form the Kingdom (biology), kingdom Plantae; they are predominantly Photosynthesis, photosynthetic. This means that they obtain their energy from sunlight, using chloroplasts derived from endosymbiosis with c ...
s, and a few
animal Animals are multicellular, eukaryotic organisms in the Biology, biological Kingdom (biology), kingdom Animalia (). With few exceptions, animals heterotroph, consume organic material, Cellular respiration#Aerobic respiration, breathe oxygen, ...
lineages. The biosyntheses of polyketides share striking similarities with
fatty acid In chemistry, in particular in biochemistry, a fatty acid is a carboxylic acid with an aliphatic chain, which is either saturated and unsaturated compounds#Organic chemistry, saturated or unsaturated. Most naturally occurring fatty acids have an ...
biosynthesis. The PKS genes for a certain polyketide are usually organized in one
operon In genetics, an operon is a functioning unit of DNA containing a cluster of genes under the control of a single promoter. The genes are transcribed together into an mRNA strand and either translated together in the cytoplasm, or undergo splic ...
or in
gene cluster A gene cluster is a group of two or more genes found within an organism's DNA that encode similar peptide, polypeptides or proteins which collectively share a generalized function and are often located within a few thousand base pairs of each othe ...
s. Type I and type II PKSs form either large modular protein complexes or dissociable molecular assemblies; type III PKSs exist as smaller homodimeric proteins.


Classification

PKSs can be classified into three types: * Type I PKSs are large, complex protein structures with multiple modules which in turn consist of several domains that are usually covalently connected to each other and fulfill different catalytic steps. The minimal composition of a type I PKS module consists of an acyltransferase (AT) domain, which is responsible for choosing the building block to be used, a keto synthase (KS) domain, which catalyzes the C-C bond formation and an acyl carrier protein (ACP) domain, also known as thiolation domain. The latter contains a conserved Ser residue, post-translationally modified with a phosphopantetheine at the end of which the polyketide chain is covalently bound during biosynthesis as a thioester. Moreover, multiple other optional domains can also exist within a module like ketoreductase or dehydratase domains which alter the default 1,3-dicarbonyl functionality of the installed ketide by sequential reduction to an alcohol and double bond, respectively. These domains work together like an assembly line. This type of type I PKSs is also referred to as cis-acyltransferase polyketide synthases (cis-AT PKSs). In contrast to that, so called trans-AT PKSs evolved independently and lack AT domains in their modules. This activity is provided by free-standing AT domains instead. Moreover, they often contain uncommon domains with unique catalytic activities. *Type II PKSs behave very similarly to type I PKS but with one key difference: Instead of one large megaenzyme, type II PKSs are separate, monofunctional enzymes. The smallest possible type II PKS consists of an ACP, as well as two heterodimeric KS units (KSα, which catalyzes the C-C bond formation and KSβ, also known as 'chain length factor' — CLF, since it can determine the carbon chain length), which fulfill a similar function as the AT, KS and ACP domains in type I PKSs, even though type II PKSs are lacking a separate AT domain. Additionally, type II PKSs often work iteratively where multiple chain elongation steps are carried out by the same enzyme, similar to type III PKSs. *Type III PKSs are small homodimers of 40 kDa proteins that combine all the activities from the essential type I and II PKS domains. However, in contrast to type I and II PKSs they do not require an ACP-bound substrate. Instead, they can use a free acyl-CoA substrate for chain elongation. Moreover, type III PKSs contain a Cys-His-Asn catalytic triad in their active center, with the cysteine residue acting as the attacking nucleophile, whereas type I and II PKSs are characterized by a Cys-His-His catalytic triad. Typical products of type III PKSs include phenolic lipids like alkylresorcinols *In addition to these three types of PKSs, they can be further classified as iterative or noniterative. Iterative Type II PKSs reuse domains in a cyclic fashion. Other classifications include the degree of reduction performed during the synthesis of the growing polyketide chain. ** NR-PKSs — non- reducing PKSs, the products of which are true polyketides ** PR-PKSs — partially reducing PKSs ** FR-PKSs — fully reducing PKSs, the products of which are
fatty acid In chemistry, in particular in biochemistry, a fatty acid is a carboxylic acid with an aliphatic chain, which is either saturated and unsaturated compounds#Organic chemistry, saturated or unsaturated. Most naturally occurring fatty acids have an ...
derivatives


Modules and domains

Each type I polyketide-synthase module consists of several domains with defined functions, separated by short spacer regions. The order of modules and domains of a complete polyketide-synthase is as follows (in the order
N-terminus The N-terminus (also known as the amino-terminus, NH2-terminus, N-terminal end or amine-terminus) is the start of a protein or polypeptide, referring to the free amine group (-NH2) located at the end of a polypeptide. Within a peptide, the amin ...
to
C-terminus The C-terminus (also known as the carboxyl-terminus, carboxy-terminus, C-terminal tail, carboxy tail, C-terminal end, or COOH-terminus) is the end of an amino acid chain (protein Proteins are large biomolecules and macromolecules that comp ...
): * ''Starting'' or ''loading'' module: AT-ACP- * ''Elongation'' or ''extending'' modules: -KS-AT- H-ER-KRACP- * ''Termination'' or ''releasing'' domain: -TE Domains: * AT:
Acyltransferase Acyltransferase is a type of transferase enzyme that acts upon acyl In chemistry, an acyl group is a moiety derived by the removal of one or more hydroxyl groups from an oxoacid, including inorganic acids. It contains a double-bonded oxygen ...
* ACP: Acyl carrier protein with an SH group on the cofactor, a
serine Serine (symbol Ser or S) is an α-amino acid that is used in the biosynthesis of proteins. It contains an α- amino group (which is in the protonated − form under biological conditions), a carboxyl group (which is in the deprotonated − ...
-attached 4'- phosphopantetheine * KS:
Keto-synthase Ketoacyl synthases (KSs) catalyze the condensation reaction of acyl-CoA or acyl-acyl ACP with malonyl-CoA to form 3-ketoacyl-CoA or with malonyl-ACP to form 3-ketoacyl-ACP. This reaction is a key step in the fatty acid synthesis cycle, as the resul ...
with an SH group on a
cysteine Cysteine (; symbol Cys or C) is a semiessential proteinogenic amino acid with the chemical formula, formula . The thiol side chain in cysteine enables the formation of Disulfide, disulfide bonds, and often participates in enzymatic reactions as ...
side-chain * KR: Ketoreductase * DH: Dehydratase * ER: Enoylreductase * MT: Methyltransferase O- or C- (α or β) * SH: PLP-dependent cysteine lyase * TE: Thioesterase The polyketide chain and the starter groups are bound with their carboxy
functional group In organic chemistry, a functional group is any substituent or moiety (chemistry), moiety in a molecule that causes the molecule's characteristic chemical reactions. The same functional group will undergo the same or similar chemical reactions r ...
to the SH groups of the ACP and the KS domain through a
thioester In organic chemistry, thioesters are organosulfur compounds with the molecular structure . They are analogous to carboxylate esters () with the sulfur in the thioester replacing oxygen in the carboxylate ester, as implied by the thio- prefix ...
linkage: R- C(= O) O H + H S-protein <=> R- C(= O) S-protein + H2O. The ACP carrier domains are similar to the PCP carrier domains of nonribosomal peptide synthetases, and some proteins combine both types of modules.


Stages

The growing chain is handed over from one
thiol In organic chemistry, a thiol (; ), or thiol derivative, is any organosulfur compound of the form , where R represents an alkyl or other organic substituent. The functional group itself is referred to as either a thiol group or a sulfhydryl grou ...
group to the next by trans-acylations and is released at the end by
hydrolysis Hydrolysis (; ) is any chemical reaction in which a molecule of water breaks one or more chemical bonds. The term is used broadly for substitution reaction, substitution, elimination reaction, elimination, and solvation reactions in which water ...
or by cyclization (
alcoholysis In chemistry, solvolysis is a type of nucleophilic substitution (S1/S2) or elimination where the nucleophile is a solvent molecule. Characteristic of S1 reactions, solvolysis of a chiral reactant affords the racemate. Sometimes however, the ster ...
or
aminolysis In chemistry, aminolysis (/am·i·nol·y·sis/) is any chemical reaction in which a molecule is Chemical decomposition, lysed (split into two parts) by reacting with ammonia () or an amine. The case where the reaction involves ammonia may be more ...
). Starting stage: * The starter group, usually
acetyl-CoA Acetyl-CoA (acetyl coenzyme A) is a molecule that participates in many biochemical reactions in protein, carbohydrate and lipid metabolism. Its main function is to deliver the acetyl group to the citric acid cycle (Krebs cycle) to be oxidation, o ...
or its analogues, is loaded onto the ACP domain of the starter module catalyzed by the starter module's AT domain. Elongation stages: * The polyketide chain is handed over from the ACP domain of the previous module to the KS domain of the current module, catalyzed by the KS domain. * The elongation group, usually malonyl-CoA or methylmalonyl-CoA, is loaded onto the current ACP domain catalyzed by the current AT domain. * The ACP-bound elongation group reacts in a Claisen condensation with the KS-bound polyketide chain under CO2 evolution, leaving a free KS domain and an ACP-bound elongated polyketide chain. The reaction takes place at the KSn-bound end of the chain, so that the chain moves out one position and the elongation group becomes the new bound group. * Optionally, the fragment of the polyketide chain can be altered stepwise by additional domains. The KR (keto-reductase) domain reduces the β-keto group to a β-hydroxy group, the DH (dehydratase) domain splits off H2O, resulting in the α-β- unsaturated alkene, and the ER (enoyl-reductase) domain reduces the α-β-double- bond to a single-bond. These modification domains actually affect the previous addition to the chain (i.e. the group added in the previous module), not the component recruited to the ACP domain of the module containing the modification domain. * This cycle is repeated for each elongation module. Termination stage: * The TE domain hydrolyzes the completed polyketide chain from the ACP-domain of the previous module.


Pharmacological relevance

Polyketide synthases are an important source of naturally occurring small molecules used for chemotherapy. For example, many of the commonly used antibiotics, such as
tetracycline Tetracycline, sold under various brand names, is an antibiotic in the tetracyclines family of medications, used to treat a number of infections, including acne, cholera, brucellosis, plague, malaria, and syphilis. It is available in oral an ...
and
macrolides Macrolides are a class of mostly natural products with a large macrocycle, macrocyclic lactone ring to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides belong to the polyketide class of natural prod ...
, are produced by polyketide synthases. Other industrially important polyketides are sirolimus (immunosuppressant),
erythromycin Erythromycin is an antibiotic used for the treatment of a number of bacterial infections. This includes respiratory tract infections, skin infections, chlamydia infections, pelvic inflammatory disease, and syphilis. It may also be used ...
(antibiotic),
lovastatin Lovastatin, sold under the brand name Mevacor among others, is a statin medication, to treat high blood cholesterol and reduce the risk of cardiovascular disease. Its use is recommended together with lifestyle changes. It is taken by mouth. ...
(anticholesterol drug), and epothilone B (anticancer drug). Polyketides are a large family of natural products widely used as drugs, pesticides, herbicides, and biological probes. There are antifungal and antibacterial polyketide compounds, namely ophiocordin and ophiosetin. And are researched for the synthesis of biofuels and industrial chemicals.


Ecological significance

Only about 1% of all known molecules are natural products, yet it has been recognized that almost two thirds of all drugs currently in use are at least in part derived from a natural source. This bias is commonly explained with the argument that natural products have co-evolved in the environment for long time periods and have therefore been pre-selected for active structures. Polyketide synthase products include lipids with antibiotic, antifungal, antitumor, and predator-defense properties; however, many of the polyketide synthase pathways that bacteria, fungi and plants commonly use have not yet been characterized. Methods for the detection of novel polyketide synthase pathways in the environment have therefore been developed. Molecular evidence supports the notion that many novel polyketides remain to be discovered from bacterial sources.


See also

* Doxorubicin


References


External links

* {{Portal bar, Biology, border=no EC 6.4