8CXL

Structure of NapH3, a vanadium-dependent haloperoxidase homolog catalyzing the stereospecific alpha-hydroxyketone rearrangement reaction in napyradiomycin biosynthesis

Summary for 8CXL

• Entry DOI: 10.2210/pdb8cxl/pdb
• Related: 3w35 3w36
• Descriptor: NapH3, MAGNESIUM ION, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: vanadium-dependent haloperoxidase, vhpo, alpha-hydroxyketone rearrangement, napyradiomycin, biosynthetic protein
• Biological source: Streptomyces sp. CNQ-525
• Total number of polymer chains: 2
• Total formula weight: 103610.02

Authors

Chen, P.Y.-T.,Chekan, J.R.,Moore, B.S. (deposition date: 2022-05-21, release date: 2022-08-31, Last modification date: 2023-10-18)

Primary citation

Chen, P.Y.,Adak, S.,Chekan, J.R.,Liscombe, D.K.,Miyanaga, A.,Bernhardt, P.,Diethelm, S.,Fielding, E.N.,George, J.H.,Miles, Z.D.,Murray, L.A.M.,Steele, T.S.,Winter, J.M.,Noel, J.P.,Moore, B.S.
Structural Basis of Stereospecific Vanadium-Dependent Haloperoxidase Family Enzymes in Napyradiomycin Biosynthesis.
Biochemistry, 61:1844-1852, 2022

PubMed Abstract: Vanadium-dependent haloperoxidases (VHPOs) from bacteria differ from their counterparts in fungi, macroalgae, and other bacteria by catalyzing organohalogenating reactions with strict regiochemical and stereochemical control. While this group of enzymes collectively uses hydrogen peroxide to oxidize halides for incorporation into electron-rich organic molecules, the mechanism for the controlled transfer of highly reactive chloronium ions in the biosynthesis of napyradiomycin and merochlorin antibiotics sets the vanadium-dependent chloroperoxidases apart. Here we report high-resolution crystal structures of two homologous VHPO family members associated with napyradiomycin biosynthesis, NapH1 and NapH3, that catalyze distinctive chemical reactions in the construction of meroterpenoid natural products. The structures, combined with site-directed mutagenesis and intact protein mass spectrometry studies, afforded a mechanistic model for the asymmetric alkene and arene chlorination reactions catalyzed by NapH1 and the isomerase activity catalyzed by NapH3. A key lysine residue in NapH1 situated between the coordinated vanadate and the putative substrate binding pocket was shown to be essential for catalysis. This observation suggested the involvement of the ε-NH, possibly through formation of a transient chloramine, as the chlorinating species much as proposed in structurally distinct flavin-dependent halogenases. Unexpectedly, NapH3 is modified post-translationally by phosphorylation of an active site His (τ-pHis) consistent with its repurposed halogenation-independent, α-hydroxyketone isomerase activity. These structural studies deepen our understanding of the mechanistic underpinnings of VHPO enzymes and their evolution as enantioselective biocatalysts.

PubMed: 35985031
DOI: 10.1021/acs.biochem.2c00338

Experimental method

X-RAY DIFFRACTION (1.98 Å)