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This paper reports the crystal structure of the region of DEBS module 1 that spans the AT and ACP domains. It includes the KR domain and a previously unclassified 'linker'; the latter turns out to be a structural subdomain of the KR. The paper facilitates redefinition of the boundaries of the KR domain.
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The high resolution structure of the [KS][AT] didomain of DEBS module 5 revealed the architectural organization of the core domains of all PKS modules and offered an atomic level insight into the specific role played by the different classes of linkers in mediating interdomain interactions. The structure also demonstrated that the prevailing 'swinging arm' model for interaction between ACP and partner domains is inadequate, thereby highlighting a need for large conformational changes during the PKS catalytic cycle.
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Tang Y., Kim C.Y., Mathews I.I., Cane D.E., and Khosla C. The 2.7-Angstrom crystal structure of a 194-kDa homodimeric fragment of the 6-deoxyerythronolide B synthase. Proc Natl Acad Sci U S A 103 (2006) 11124-11129. The high resolution structure of the [KS][AT] didomain of DEBS module 5 revealed the architectural organization of the core domains of all PKS modules and offered an atomic level insight into the specific role played by the different classes of linkers in mediating interdomain interactions. The structure also demonstrated that the prevailing 'swinging arm' model for interaction between ACP and partner domains is inadequate, thereby highlighting a need for large conformational changes during the PKS catalytic cycle.
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The paper reported the solution NMR structure of the ACP domain of DEBS module 2. Its close sequence identity to other ACP domains of DEBS enabled the authors to compare and contrast the electrostatic and steric differences within this set of ACP domains.
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This paper reports the crystal structure of the [KS][AT] fragment of DEBS module 3 bound to a covalently bound inhibitor to enable clearer visualization of the KS active site.
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Showed that some protein-protein interactions between carrier protein domains and partner domains in non-ribosomal peptide synthetases (NRPSs, a related enzymatic assembly line) enabled the selection of one conformation of the carrier protein from a pre-existing equilibrium, highlighting the dynamic nature of these domains.
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Koglin A., Mofid M.R., Lohr F., Schafer B., Rogov V.V., Blum M.M., Mittag T., Marahiel M.A., Bernhard F., and Dotsch V. Conformational switches modulate protein interactions in peptide antibiotic synthetases. Science 312 (2006) 273-276. Showed that some protein-protein interactions between carrier protein domains and partner domains in non-ribosomal peptide synthetases (NRPSs, a related enzymatic assembly line) enabled the selection of one conformation of the carrier protein from a pre-existing equilibrium, highlighting the dynamic nature of these domains.
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Dynamic thiolation-thioesterase structure of a non-ribosomal peptide synthetase
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This paper reported the structures of the dynamic complexes between apo carrier protein domain and the thioesterase domain of the EntF NRPS subunit of enterobactin synthetase.
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This paper reported the structures of dynamic complexes between a carrier protein domain and a stand-alone type II thioesterase (from the third module of tyrocidine A synthetase and surfactin synthetase systems, respectively), thereby highlighting the dynamic nature of these domains.
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This paper reported the complete deconstruction of DEBS module 3, which facilitated examination of the relative importance of specific domain-domain and domain-linker interactions.
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This papers describes the remarkable range of specificity exhibited by KS and ACP domains in chain elongation. The insight gained thereby allowed the rational engineering of a kinetically competent hybrid module.
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Chen A.Y., Schnarr N.A., Kim C.Y., Cane D.E., and Khosla C. Extender unit and acyl carrier protein specificity of ketosynthase domains of the 6-deoxyerythronolide B synthase. J Am Chem Soc 128 (2006) 3067-3074. This papers describes the remarkable range of specificity exhibited by KS and ACP domains in chain elongation. The insight gained thereby allowed the rational engineering of a kinetically competent hybrid module.
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Biochemical analysis of the substrate specificity of the beta-ketoacyl-acyl carrier protein synthase domain of module 2 of the erythromycin polyketide synthase
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Utilizing a series of biochemical assays, the authors quantitatively examined the two consecutive reactions catalyzed by the KS domain - intermodular chain transfer by self-acylation and intramodular chain elongation by decarboxylative condensation - for a panel of di- and tri-ketide substrates. This analysis revealed clear but as yet unexplained differences in the specificity of the same KS domain for the two core reactions.
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Wu J., Kinoshita K., Khosla C., and Cane D.E. Biochemical analysis of the substrate specificity of the beta-ketoacyl-acyl carrier protein synthase domain of module 2 of the erythromycin polyketide synthase. Biochemistry 43 (2004) 16301-16310. Utilizing a series of biochemical assays, the authors quantitatively examined the two consecutive reactions catalyzed by the KS domain - intermodular chain transfer by self-acylation and intramodular chain elongation by decarboxylative condensation - for a panel of di- and tri-ketide substrates. This analysis revealed clear but as yet unexplained differences in the specificity of the same KS domain for the two core reactions.
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(2004)
Biochemistry
, vol.43
, pp. 16301-16310
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Wu, J.1
Kinoshita, K.2
Khosla, C.3
Cane, D.E.4
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0142149140
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Understanding substrate specificity of polyketide synthase modules by generating hybrid multimodular synthases
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Watanabe K., Wang C.C., Boddy C.N., Cane D.E., and Khosla C. Understanding substrate specificity of polyketide synthase modules by generating hybrid multimodular synthases. J Biol Chem 278 (2003) 42020-42026
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(2003)
J Biol Chem
, vol.278
, pp. 42020-42026
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Watanabe, K.1
Wang, C.C.2
Boddy, C.N.3
Cane, D.E.4
Khosla, C.5
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