Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structure and catalytic mechanism of the evolutionarily unique bacterial chalcone isomerase.
Journal, issue, pages	Acta Crystallogr D Biol Crystallogr, Vol. 71, Issue Pt 4, Page 907-917, Year 2015
Publish date	Mar 27, 2015
Authors	Maren Thomsen / Anne Tuukkanen / Jonathan Dickerhoff / Gottfried J Palm / Hanna Kratzat / Dmitri I Svergun / Klaus Weisz / Uwe T Bornscheuer / Winfried Hinrichs /
PubMed 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 ...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.
External links	Acta Crystallogr D Biol Crystallogr / PubMed:25849401
Methods	SAS (X-ray synchrotron) / X-ray diffraction
Resolution	1.8 - 2 Å
Structure data	SASDAL6: Wild-type chalcone isomerase, ligand-free (Bacterial chalcone isomerase, CHI) Method: SAXS/SANS SASDAM6: Naringenin-bound chalcone isomerase (Chalcone isomerase with Naringenin, naringenin-CHI) Method: SAXS/SANS SASDAN6: Chalcone isomerase, CHI_Δlid construct (Chalcone isomerase deltaLid, CHI_Δlid) Method: SAXS/SANS PDB-4c9s: BACTERIAL CHALCONE ISOMERASE IN open CONFORMATION FROM EUBACTERIUM RAMULUS AT 1.8 A RESOLUTION Method: X-RAY DIFFRACTION / Resolution: 1.8 Å PDB-4c9t: BACTERIAL CHALCONE ISOMERASE IN open CONFORMATION FROM EUBACTERIUM RAMULUS AT 2.0 A RESOLUTION, SelenoMet derivative Method: X-RAY DIFFRACTION / Resolution: 1.98 Å PDB-4d06: Bacterial chalcone isomerase complexed with naringenin Method: X-RAY DIFFRACTION / Resolution: 2.0 Å
Chemicals	ChemComp-GOL: GLYCEROL ChemComp-CL: Unknown entry ChemComp-SO4: SULFATE ION ChemComp-HOH: WATER ChemComp-NAR: NARINGENIN ChemComp-X8W: (2E)-3-(4-hydroxyphenyl)-1-(2,4,6-trihydroxyphenyl)prop-2-en-1-one
Source	eubacterium ramulus (bacteria)
Keywords	ISOMERASE / FLAVONOIDS / BACTERIAL CHALCONE ISOMERASE / NARINGENIN