6DA7

Crystal structure of the TtnD decarboxylase from the tautomycetin biosynthesis pathway of Streptomyces griseochromogenes with apo form at 1.83 A resolution (I222)

Summary for 6DA7

• Entry DOI: 10.2210/pdb6da7/pdb
• Related: 6DA6 6DA9
• Descriptor: UbiD-like decarboxylase, SODIUM ION, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ... (6 entities in total)
• Functional Keywords: ttnd, decarboxylase, tautomycetin biosynthesis, prfmn binding, lyase, structural genomics, psi-biology, enzyme discovery for natural product biosynthesis, natpro
• Biological source: Streptomyces griseochromogenes
• Total number of polymer chains: 1
• Total formula weight: 56702.36

Authors

Han, L.,Rudolf, J.D.,Chang, C.-Y.,Miller, M.D.,Soman, J.,Phillips Jr., G.N.,Shen, B.,Enzyme Discovery for Natural Product Biosynthesis (NatPro) (deposition date: 2018-05-01, release date: 2018-10-03, Last modification date: 2023-10-04)

Primary citation

Annaval, T.,Han, L.,Rudolf, J.D.,Xie, G.,Yang, D.,Chang, C.Y.,Ma, M.,Crnovcic, I.,Miller, M.D.,Soman, J.,Xu, W.,Phillips Jr., G.N.,Shen, B.
Biochemical and Structural Characterization of TtnD, a Prenylated FMN-Dependent Decarboxylase from the Tautomycetin Biosynthetic Pathway.
ACS Chem. Biol., 13:2728-2738, 2018

PubMed Abstract: Tautomycetin (TTN) is a polyketide natural product featuring a terminal alkene. Functional characterization of the genes within the ttn gene cluster from Streptomyces griseochromogenes established the biosynthesis of the TTN polyketide backbone, its dialkylmaleic anhydride moiety, the coupling of the two moieties to form the nascent intermediate TTN F-1, and the tailoring steps converting TTN F-1 to TTN. Here, we report biochemical and structural characterization of TtnD, a prenylated FMN (prFMN)-dependent decarboxylase belonging to the UbiD family that catalyzes the penultimate step of TTN biosynthesis. TtnD catalyzes decarboxylation of TTN D-1 to TTN I-1, utilizing prFMN as a cofactor generated by the TtnC flavin prenyltransferase; both TtnD and TtnC are encoded within the ttn biosynthetic gene cluster. TtnD exhibits substrate promiscuity but accepts only TTN D-1 congeners that feature an α,β-unsaturated acid, supporting the [3+2] cycloaddition mechanism during catalysis that requires the double bond of an α,β-unsaturated acid substrate. TtnD shares a similar overall structure with other members of the UbiD family but forms a homotetramer in solution. Each protomer is composed of three domains with the active site located between the middle and C-terminal domains; R169-E272-E277, constituting the catalytic triad, and E228, involved in Mn(II)-mediated binding of prFMN, were confirmed by site-directed mutagenesis. TtnD represents the first example of a prFMN-dependent decarboxylase involved in polyketide biosynthesis, expanding the substrate scope of the UbiD family of decarboxylases beyond simple aromatic and cinnamic acids. TtnD and its homologues are widespread in nature and could be exploited as biocatalysts for organic synthesis.

PubMed: 30152678
DOI: 10.1021/acschembio.8b00673

Experimental method

X-RAY DIFFRACTION (1.83 Å)