The catalytic mechanism of the marine-derived macrocyclase PatGmac
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Cyclic peptides are a class of compounds with high therapeutic potential, possessing bioactivities including antitumor and antiviral (including anti-HIV). Despite their desirability, efficient design and production of these compounds has not been achieved to date. The catalytic mechanism of patellamide macrocyclization by the PatG macrocyclase domain has been computationally investigated by using quantum mechanics/molecular mechanics methodology, specifically ONIOM(M06/6-311++G(2d,2p):ff94//B3LYP/6-31G(d):ff94). The mechanism proposed herein begins with a proton transfer from Ser783 to His 618 and from the latter to Asp548. Nucleophilic attack of Ser783 on the substrate leads to the formation of an acyl–enzyme covalent complex. The leaving group Ala-Tyr-Asp-Gly (AYDG) of the substrate is protonated by the substrate's N terminus, leading to the breakage of the P1−P1′ bond. Finally, the substrate's N terminus attacks the P1 residue, decomposing the acyl–enzyme complex forming the macrocycle. The formation and decomposition of the acyl–enzyme complex have the highest activation free energies (21.1 kcal mol−1 and 19.8 kcal mol−1 respectively), typical of serine proteases. Understanding the mechanism behind the macrocyclization of patellamides will be important to the application of the enzymes in the pharmaceutical and biotechnological industries.
Brás , N F , Ferreira , P , Calixto , A R , Jaspars , M , Houssen , W , Naismith , J , Fernandes , P A & Ramos , M J 2016 , ' The catalytic mechanism of the marine-derived macrocyclase PatGmac ' Chemistry - A European Journal , vol. 22 , no. 37 , pp. 13089–13097 . DOI: 10.1002/chem.201601670
Chemistry - A European Journal
© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. This work is made available online in accordance with the publisher’s policies. This is the author created, accepted version manuscript following peer review and may differ slightly from the final published version. The final published version of this work is available at https://dx.doi.org/10.1002/chem.201601670© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. This work is made available online in accordance with the publisher’s policies. This is the author created, accepted version manuscript following peer review and may differ slightly from the final published version. The final published version of this work is available at https://dx.doi.org/10.1002/chem.201601670
DescriptionThis work received financial support from the European Union (FEDER funds through COMPETE) and National Funds (Fundação para a Ciência e Tecnologia, FCT) through Projects EXCL/QEQ-COM/0394/2012, EXCL-II/QEQ-COM/0394/2012, and Pest-C/EQB/LA0006/2013. N.F.B. would like to thank the FCT for her IF starting grant (IF/01355/2014).
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