Cyanobacterial Polyketide Synthase Docking Domains: A Tool for Engineering Natural Product Biosynthesis

Whicher, Jonathan R.; Smaga, Sarah; Hansen, Douglas A.; Brown, William Clay; Gerwick, William H.; Sherman, David H.; Smith, Janet L.

doi:10.1016/j.chembiol.2013.09.015

Cited by 110 publications

(210 citation statements)

References 48 publications

Supporting

Mentioning

190

Contrasting

Unclassified

Order By: Relevance

“…Nor is the ACP D docking site on HMGS analogous to either of the ACP-KS docking sites observed in cryo-EM maps of a PKS module (19). We find no evidence of a second active site entrance in the HMGS structure (for example, poorly ordered loops that could expose the active site, as in the KS) (19,21,35,36). We conclude that ACP A and ACP D insert acyl-Ppant through the same active site entrance, as do the donor and acceptor-CoAs of HMGCS, but that the ACPs interact with different regions of the HMGS surface.…”

Section: Discussionmentioning

confidence: 52%

“…A critical question is whether the ACPs engage HMGS simultaneously or sequentially. The affinity of HMGS for ACP D is tenfold greater than a native docking domain pair (K d = 0.5 μM vs. 5-25 μM) (20,21). HMGS has lower affinity for ACP A than for ACP D , based on the K d of 150-200 μM for the bryostatin HMGS and its cognate ACP A (15).…”

Section: Discussionmentioning

confidence: 99%

“…The homologous KS extension enzymes distinguish their cognate donor and acceptor ACPs through two active site entrances (19) in interactions facilitated by fusion or noncovalent interaction of appended docking domains (20,21), which are absent in HMGS. (Table 1).…”

Section: Significancementioning

confidence: 99%

See 2 more Smart Citations

Anatomy of the β-branching enzyme of polyketide biosynthesis and its interaction with an acyl-ACP substrate

Maloney

Gerwick

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Alkyl branching at the β position of a polyketide intermediate is an important variation on canonical polyketide natural product biosynthesis. The branching enzyme, 3-hydroxy-3-methylglutaryl synthase (HMGS), catalyzes the aldol addition of an acyl donor to a β-keto-polyketide intermediate acceptor. HMGS is highly selective for two specialized acyl carrier proteins (ACPs) that deliver the donor and acceptor substrates. The HMGS from the curacin A biosynthetic pathway (CurD) was examined to establish the basis for ACP selectivity. The donor ACP (CurB) had high affinity for the enzyme (K d = 0.5 μM) and could not be substituted by the acceptor ACP. Highresolution crystal structures of HMGS alone and in complex with its donor ACP reveal a tight interaction that depends on exquisite surface shape and charge complementarity between the proteins. Selectivity is explained by HMGS binding to an unusual surface cleft on the donor ACP, in a manner that would exclude the acceptor ACP. Within the active site, HMGS discriminates between pre-and postreaction states of the donor ACP. The free phosphopantetheine (Ppant) cofactor of ACP occupies a conserved pocket that excludes the acetyl-Ppant substrate. In comparison with HMG-CoA (CoA) synthase, the homologous enzyme from primary metabolism, HMGS has several differences at the active site entrance, including a flexible-loop insertion, which may account for the specificity of one enzyme for substrates delivered by ACP and the other by CoA.natural products | polyketide synthase | curacin | HMG synthase | acyl carrier protein P olyketides are a large and chemically diverse group of natural products that includes many pharmaceuticals with a broad range of biological activities and applications as antibiotics, antifungals, antiinflammatory drugs, and cancer chemotherapeutic agents (1). Polyketide synthase (PKS) biosynthetic pathways are subjects of efforts to engineer diversification of natural products in pursuit of pharmaceutical leads and compounds of industrial importance (2). They are rich sources for development of chemoenzymatic catalysts based on PKS enzymes with unusual catalytic activities.Modular type I PKS pathways, among the most versatile of nature's systems, are biosynthetic assembly lines composed of modules that act in a defined sequence to produce complex products with a variety of functional groups and chiral centers. Each module is a set of fused catalytic domains that extend and modify a polyketide intermediate. Biosynthesis proceeds from intermediates tethered to acyl carrier protein (ACP) domains via a thioester link to a phosphopantetheine (Ppant) cofactor. A ketosynthase (KS) domain catalyzes extension of the intermediate, and subsequent modification domains typically catalyze reduction and/or methylation of the β-keto (3-keto) extension product. Beyond the enzymes for these core reactions, many PKS pathways also include other catalytic functionality. Among the most interesting of these noncanonical capabilities is alkylation at the β position by a set of β...

show abstract

Section: Discussionmentioning

confidence: 52%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Anatomy of the β-branching enzyme of polyketide biosynthesis and its interaction with an acyl-ACP substrate

Maloney

Gerwick

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…Pieces incorporating both PKS and NRPS modules are of particular interest, given the reported differences in their oligomerization states 16,18 . In terms of communication across intersubunit interfaces (in trans), key insights have emerged from the structures of excised 'docking domains' [42][43][44] . However, it will be important in future to visualize several more complete interfaces comprising not only the docking elements but also the flanking domains, as achieved for Pik module 5 (ref.…”

Section: Discussionmentioning

confidence: 99%

“…It took over a decade to complete the catalog of commonly found domain structures from cis-AT PKSs, which were solved either by X-ray crystallography (didomain KS-AT 27,28 , KR 29-35 , DH 36,37 and didomain KR-ER 33 ) or, in the case of the ACPs 38-40 , by NMR. Other fragments characterized at high resolution include a region lying between the AT and KR domains of many PKS modules, which appears to serve as an internal dimerization motif 41 , and short sequences at the extreme C-and N-terminal ends of the subunits (referred to as 'docking domains'), which function as intermolecular recognition elements [42][43][44] .…”

Section: The Dissection Approach To Studying Functional Domainsmentioning

confidence: 99%

The structural biology of biosynthetic megaenzymes

Weissman¹

2015

Nat Chem Biol

191

165

View full text Add to dashboard Cite

The modular polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) are among the largest and most complicated enzymes in nature. In these biosynthetic systems, independently folding protein domains, which are organized into units called 'modules', operate in assembly-line fashion to construct polymeric chains and tailor their functionalities. Products of PKSs and NRPSs include a number of blockbuster medicines, and this has motivated researchers to understand how they operate so that they can be modified by genetic engineering. Beginning in the 1990s, structural biology has provided a number of key insights. The emerging picture is one of remarkable dynamics and conformational programming in which the chemical states of individual catalytic domains are communicated to the others, configuring the modules for the next stage in the biosynthesis. This unexpected level of complexity most likely accounts for the low success rate of empirical genetic engineering experiments and suggests ways forward for productive megaenzyme synthetic biology.

show abstract

Polyketidsynthase‐Module: eine Neudefinition

Keatinge‐Clay

2017

Angewandte Chemie

View full text Add to dashboard Cite

Biosynthese ·Enzymologie ·E volutionsgeleitetes Engineering ·Module ·PolyketideSeit vor 27 Jahren die Sequenz der enzymatischen Biosynthesemaschinerie fürd en Aufbau des Kohlenstoffgerüsts des Polyketid-Antibiotikums Erythromycin bestimmt wurde, nennt man Gruppen von Domänen, die sich innerhalb solcher Polyketidsynthasen (PKSs) wiederholen, "Module", in Analogie zur Domänenanordnung in der Fettsäuresynthase von Säugetieren. [1] Vorkurzem berichteten Abe und Mitarbeiter, dass die Domänengruppen, die in der Evolution der PKS-Biosynthesemaschinerie genetisch gemeinsam migrieren, nicht unter diese Definition fallen. [2] Studenten hçren oft erstmals von modularen PKSs in einführenden Biochemiekursen im Zusammenhang der Palmitat-Biosynthese durch die Fettsäuresynthase aus Säugetieren. [3] Sie erfahren, dass Enzymdomänen mit Acyl-Carrier-Protein(ACP)-Domänen kooperieren, um eine Starter-Acylgruppe mit Kohlenstoffverlängerungseinheiten zu elongieren und eine längere Acylkette zu generieren, deren chemische Eigenschaften von den Enzymen eingestellt werden, mit denen sie während ihrer Synthese interagiert. Eine Acyltransferase (AT) selektiert das Monomer,d as von einer Ketosynthase (KS) an die wachsende Kette kondensiert wird, und prozessierende Enzyme modifizieren den Bereich um die so gebildete b-Ketogruppe.Die prozessierenden Enzyme der Polyketid-Biosynthesemaschinerie sind äquivalent zu jenen der Säuger-Fettsäuresynthase,i nd er eine Ketoreduktase (KR) die b-Ketogruppe stereoselektiv reduziert, eine Dehydratase (DH) die resultierende b-Hydroxygruppe dehydratisiert und eine Enoylreduktase (ER) den b-Kohlenstoff zu einer Methylengruppe reduziert. Eine Thioesterase (TE) am C-Terminus dieser Synthasen setzt das Endprodukt üblicherweise durch Hydrolyse oder Cyclisierung frei. Da die Domänen der Säuger-Fettsäuresynthase gemäßK S + AT + DH + ER + KR + ACP + TE angeordnet sind, wurden die Module der Polyketid-Biosynthesemaschinerie äquivalent definiert:Beginn mit einer KS,Abschluss mit einem ACPund im Mittelbereich optionale prozessierende Enzyme.Abe und Mitarbeiter haben nun berichtet, dass in der Evolution der Biosynthesemaschineriep rozessierende Enzyme gemeinsam mit der nachgeschalteten und nicht mit der vorgeschalteten KS migrieren (Abbildung 1). Sie beobachteten dies durch Vergleich von vier der grçßten bekannten PKSs (jede 25-30 Module lang und ca. fünfmal so schwer wie das bakterielle Ribosom), welche die Aminopolyole Mediomycin, Neomediomycin, ECO-02301 und Neotetrafibricin [*] Prof. A. T.

show abstract

Cyanobacterial Polyketide Synthase Docking Domains: A Tool for Engineering Natural Product Biosynthesis

Cited by 110 publications

References 48 publications

Anatomy of the β-branching enzyme of polyketide biosynthesis and its interaction with an acyl-ACP substrate

Anatomy of the β-branching enzyme of polyketide biosynthesis and its interaction with an acyl-ACP substrate

The structural biology of biosynthetic megaenzymes

Polyketidsynthase‐Module: eine Neudefinition

Contact Info

Product

Resources

About