The Structure of Docking Domains in Modular Polyketide Synthases

Broadhurst, R. William; Nietlispach, Daniel; Wheatcroft, Michael; Leadlay, Peter F.; Weissman, Kira J.

doi:10.1016/s1074-5521(03)00156-x

Cited by 209 publications

(365 citation statements)

References 33 publications

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“…The PKS di-domain structure includes a portion of the N-terminal docking domain, which is its "ticket" to molecular recognition and association with the preceding PKS module. The coiled-coil helices at the dimer axis are consistent with an NMR structure of the isolated docking domains (13), demonstrating that the basis for successful docking is formation of a four-helix bundle with the C-terminus of the previous module. The emerging model of docking domains is also consistent with the emerging model of a common architecture for PKS modules and the type I FAS.…”

Section: Viewsupporting

confidence: 67%

Clearing the Skies over Modular Polyketide Synthases

Sherman

Smith

2006

ACS Chem. Biol.

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Modular polyketide synthases (PKSs) are large multifunctional proteins that synthesize complex polyketide metabolites in microbial cells. A series of recent studies confirm the close protein structural relationship between catalytic domains in the type I mammalian fatty acid synthase (FAS) and the basic synthase unit of the modular PKS. They also establish a remarkable similarity in the overall organization of the type I FAS and the PKS module. This information provides important new conclusions about catalytic domain architecture, function, and molecular recognition that are essential for future efforts to engineer useful polyketide metabolites with valuable biological activities.

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Section: Viewsupporting

confidence: 67%

Clearing the Skies over Modular Polyketide Synthases

Sherman

Smith

2006

ACS Chem. Biol.

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“…In various studies, it had been shown that matching pairs of terminal regions, referred to as docking domains or linkers, promote the correct positioning of PKSs. The structure of N-and C-terminal linkers contain two separate four ␣-helix bundles, which together mediate the specific docking interactions (20). Based on the crystal structure of the free-standing NRPS C domain VibH of vibriobactin biosynthetic system (21), as well as secondary structure predictions, NRPS COM domains are believed also to possess ␣-helical structures that may provide the interfaces for the selective recognition of partner NRPSs.…”

Section: Discussionmentioning

confidence: 99%

Selective interaction between nonribosomal peptide synthetases is facilitated by short communication-mediating domains

Hahn

Stachelhaus

2004

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

144

165

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Nonribosomal peptide synthetases (NRPSs) catalyze the formation of structurally diverse and biologically important peptides. Given their modular organization, NRPSs provide an enormous potential for biocombinatorial approaches to generate novel bioactive compounds. Crucial for the exploitation of this potential is a profound knowledge of the intermolecular communication between partner NRPSs. The overall goal of this study was to understand the basis of protein-protein communication that facilitates the selective interaction in these multienzyme complexes. On this account, we studied the relevance of short regions at the termini of the NRPSs tyrocidine (Tyc) synthetases TycA, TycB, and TycC, constituting the Tyc biosynthetic template. In vitro and in vivo investigations of C-terminal deletion mutants of the initiation module TycA provided evidence for the existence and impact of short communication-mediating (COM) domains. Their decisive role in proteinprotein recognition was subsequently proven by means of COM domain-swapping experiments. Substitution of the terminal COM domains between the donor modules TycA and TycB3, as well as between the acceptor modules TycB1 and TycC1, clearly demonstrated that matching pairs of COM domains are both necessary and sufficient for the establishment of communication between partner NRPSs in trans. These results corroborated the generality of COM domains, which were subsequently exploited to induce crosstalk, even between NRPSs derived from different biosynthetic systems. In conclusion, COM domains represent interesting tools for biocombinatorial approaches, which, for example, could be used for the generation of innovative natural product derivatives. N onribosomal peptide synthetases (NRPSs) are large multidomain enzymes responsible for the biosynthesis of many pharmacologically important bioactive compounds of great structural diversity (1-3). Prominent examples are the antibiotics penicillin, vancomycin, and actinomycin D, the immunosuppressant cyclosporine A, the siderophore enterobactin, and the antitumor drug bleomycin. As illustrated in Fig. 1 for the biosynthesis of the nonribosomal peptide (NRP) tyrocidine, NRPSs are organized into distinct modules, each of them responsible for the incorporation of one amino acid into the nascent peptide chain. A module can be further subdivided into catalytic domains, which are responsible for the coordinated recognition and activation [adenylation (A) domain] (4), covalent binding and transfer [peptidyl carrier protein (PCP) domain] (5), and incorporation [condensation (C) domain] of a certain substrate amino acid into the peptide chain (6). In addition to these so-called core domains, optional domains catalyze the modification of incorporated residues, i.e., by epimerization (E) or N-methylation (MT) domains (7). Product release is normally effected by a thioesterase (Te) domain, catalyzing the formation of linear, cyclic, or branched cyclic products, representative for the class of NRPs (8).Because of the modular organization of...

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“…5) accounts for the biophysical data presented here and is also in agreement with the previously published biochemical findings. 10,16 According to this model, the ACP2 domain docks in the deep cleft of [KS3][AT3] that is established by the KS-AT interdomain linker region. The binding sites on helix 1 of ACP2 are within 4 Å of the AT3 domain.…”

Section: Protein-protein Interactions Between Holo-acp2 and Ks3 Of Debsmentioning

confidence: 99%

“…Significantly, the location of the C-terminus of ACP2 in our model is consistent with the proposed model for the interaction between the Cterminus docking domain attached to the ACP and the N-terminal coiled coil domain present on the KS partner. 16 To ascertain whether or not the observed changes in the [ 1 H, 15 (Fig. 6).…”

Section: Protein-protein Interactions Between Holo-acp2 and Ks3 Of Debsmentioning

confidence: 99%

Probing the interactions of an acyl carrier protein domain from the 6‐deoxyerythronolide B synthase

et al. 2011

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The assembly-line architecture of polyketide synthases (PKSs) provides an opportunity to rationally reprogram polyketide biosynthetic pathways to produce novel antibiotics. A fundamental challenge toward this goal is to identify the factors that control the unidirectional channeling of reactive biosynthetic intermediates through these enzymatic assembly lines. Within the catalytic cycle of every PKS module, the acyl carrier protein (ACP) first collaborates with the ketosynthase (KS) domain of the paired subunit in its own homodimeric module so as to elongate the growing polyketide chain and then with the KS domain of the next module to translocate the newly elongated polyketide chain. Using NMR spectroscopy, we investigated the features of a structurally characterized ACP domain of the 6-deoxyerythronolide B synthase that contribute to its association with its KS translocation partner. Not only were we able to visualize selective protein-protein interactions between the two partners, but also we detected a significant influence of the acyl chain substrate on this interaction. A novel reagent, CF 3 -S-ACP, was developed as a 19 F NMR spectroscopic probe of protein-protein interactions. The implications of our findings for understanding intermodular chain translocation are discussed.

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The Structure of Docking Domains in Modular Polyketide Synthases

Cited by 209 publications

References 33 publications

Clearing the Skies over Modular Polyketide Synthases

Clearing the Skies over Modular Polyketide Synthases

Selective interaction between nonribosomal peptide synthetases is facilitated by short communication-mediating domains

Probing the interactions of an acyl carrier protein domain from the 6‐deoxyerythronolide B synthase

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