title: Structure and catalytic mechanism of the evolutionarily unique bacterial chalcone isomerase.
abstract: Flavonoids represent a large class of secondary metabolites produced by plants. These polyphenolic compounds are well known for their antioxidative abilities, are antimicrobial phytoalexins responsible for flower pigmentation to attract pollinators and, in addition to other properties, are also specific bacterial regulators governing the expression of Rhizobium genes involved in root nodulation (Firmin et al., 1986). The bacterial chalcone isomerase (CHI) from Eubacterium ramulus catalyses the first step in a flavanone-degradation pathway by ring opening of (2S)-naringenin to form naringenin chalcone. The structural biology and enzymology of plant CHIs have been well documented, whereas the existence of bacterial CHIs has only recently been elucidated. This first determination of the structure of a bacterial CHI provides detailed structural insights into the key step of the flavonoid-degradation pathway. The active site could be confirmed by co-crystallization with the substrate (2S)-naringenin. The stereochemistry of the proposed mechanism of the isomerase reaction was verified by specific (1)H/(2)H isotope exchange observed by (1)H NMR experiments and was further supported by mutagenesis studies. The active site is shielded by a flexible lid, the varying structure of which could be modelled in different states of the catalytic cycle using small-angle X-ray scattering data together with the crystallographic structures. Comparison of bacterial CHI with the plant enzyme from Medicago sativa reveals that they have unrelated folds, suggesting that the enzyme activity evolved convergently from different ancestor proteins. Despite the lack of any functional relationship, the tertiary structure of the bacterial CHI shows similarities to the ferredoxin-like fold of a chlorite dismutase and the stress-related protein SP1.
authors: Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany.
authors: Maren
authors: M
authors: Thomsen
authors: EMBL, c/o DESY, Notkestrasse 85, Gebäude 25A, 22603 Hamburg, Germany.
authors: Anne
authors: A
authors: Tuukkanen
authors: Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany.
authors: Jonathan
authors: J
authors: Dickerhoff
authors: Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany.
authors: Gottfried J
authors: GJ
authors: Palm
authors: Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany.
authors: Hanna
authors: H
authors: Kratzat
authors: EMBL, c/o DESY, Notkestrasse 85, Gebäude 25A, 22603 Hamburg, Germany.
authors: Dmitri I
authors: DI
authors: Svergun
authors: Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany.
authors: Klaus
authors: K
authors: Weisz
authors: Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany.
authors: Uwe T
authors: UT
authors: Bornscheuer
authors: Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany.
authors: Winfried
authors: W
authors: Hinrichs
mesh_terms: D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D005051:Eubacterium / Q000737:chemistry / Q000201:enzymology*; D005419:Flavonoids / Q000378:metabolism; D019753:Intramolecular Lyases / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D011487:Protein Conformation; D053838:Scattering, Small Angle; D014961:X-Ray Diffraction
chemical_list: D005419:Flavonoids; D019753:Intramolecular Lyases; C019865:chalcone isomerase
keywords: Eubacterium ramulus; SAXS; chalcone isomerase; flavonoid degradation