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Thomsen M, Tuukkanen A, Dickerhoff J, Palm GJ, Kratzat H, Svergun DI, Weisz K, Bornscheuer UT, Hinrichs W. Structure and catalytic mechanism of the evolutionarily unique bacterial chalcone isomerase. ACTA ACUST UNITED AC 2015; 71:907-17. [PMID: 25849401 DOI: 10.1107/s1399004715001935] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 01/29/2015] [Indexed: 11/10/2022]
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.
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Affiliation(s)
- Maren Thomsen
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany
| | - Anne Tuukkanen
- EMBL, c/o DESY, Notkestrasse 85, Gebäude 25A, 22603 Hamburg, Germany
| | - Jonathan Dickerhoff
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany
| | - Gottfried J Palm
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany
| | - Hanna Kratzat
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany
| | - Dmitri I Svergun
- EMBL, c/o DESY, Notkestrasse 85, Gebäude 25A, 22603 Hamburg, Germany
| | - Klaus Weisz
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany
| | - Uwe T Bornscheuer
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany
| | - Winfried Hinrichs
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany
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