title: Induced-fit upon ligand binding revealed by crystal structures of the hot-dog fold thioesterase in dynemicin biosynthesis.
abstract: Dynemicins are structurally related 10-membered enediyne natural products isolated from Micromonospora chernisa with potent antitumor and antibiotic activity. The early biosynthetic steps of the enediyne moiety of dynemicins are catalyzed by an iterative polyketide synthase (DynE8) and a thioesterase (DynE7). Recent studies indicate that the function of DynE7 is to off-load the linear biosynthetic intermediate assembled on DynE8. Here, we report crystal structures of DynE7 in its free form at 2.7 Å resolution and of DynE7 in complex with the DynE8-produced all-trans pentadecen-2-one at 2.1 Å resolution. These crystal structures reveal that upon ligand binding, significant conformational changes throughout the substrate-binding tunnel result in an expanded tunnel that traverses an entire monomer of the tetrameric DynE7 protein. The enlarged inner segment of the channel binds the carbonyl-conjugated polyene mainly through hydrophobic interactions, whereas the putative catalytic residues are located in the outer segment of the channel. The crystallographic information reinforces an unusual catalytic mechanism that involves a strictly conserved arginine residue for this subfamily of hot-dog fold thioesterases, distinct from the typical mechanism for hot-dog fold thioesterases that utilizes an acidic residue for catalysis.
authors.affiliation: School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551.
authors.forename: Chong Wai
authors.initials: CW
authors.lastname: Liew
authors.forename: Andrew
authors.initials: A
authors.lastname: Sharff
authors.forename: Masayo
authors.initials: M
authors.lastname: Kotaka
authors.forename: Rong
authors.initials: R
authors.lastname: Kong
authors.forename: Huihua
authors.initials: H
authors.lastname: Sun
authors.forename: Insaf
authors.initials: I
authors.lastname: Qureshi
authors.forename: Gérard
authors.initials: G
authors.lastname: Bricogne
authors.forename: Zhao-Xun
authors.initials: ZX
authors.lastname: Liang
authors.forename: Julien
authors.initials: J
authors.lastname: Lescar
mesh_terms: D000595:Amino Acid Sequence; D000903:Antibiotics, Antineoplastic / Q000096:biosynthesis* / Q000737:chemistry; D002384:Catalysis; D018360:Crystallography, X-Ray; D053281:Enediynes / Q000737:chemistry / Q000378:metabolism*; D008024:Ligands; D008847:Micromonospora / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009097:Multienzyme Complexes / Q000737:chemistry; D016297:Mutagenesis, Site-Directed; D048630:Polyketide Synthases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D017510:Protein Folding; D054730:Protein Interaction Domains and Motifs; D020836:Protein Structure, Quaternary; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D017386:Sequence Homology, Amino Acid; D013869:Thiolester Hydrolases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*
chemical_list: D000903:Antibiotics, Antineoplastic; D053281:Enediynes; D008024:Ligands; D009097:Multienzyme Complexes; D011994:Recombinant Proteins; D048630:Polyketide Synthases; D013869:Thiolester Hydrolases