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- PDB-4c9t: BACTERIAL CHALCONE ISOMERASE IN open CONFORMATION FROM EUBACTERIU... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4c9t | ||||||
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Title | BACTERIAL CHALCONE ISOMERASE IN open CONFORMATION FROM EUBACTERIUM RAMULUS AT 2.0 A RESOLUTION, SelenoMet derivative | ||||||
![]() | CHALCONE ISOMERASE | ||||||
![]() | ISOMERASE / FLAVONOIDS | ||||||
Function / homology | Chalcone isomerase, N-terminal / Chalcone isomerase N-terminal domain / chalcone isomerase / chalcone isomerase activity / Chalcone isomerase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Thomsen, M. / Palm, G.J. / Hinrichs, W. | ||||||
![]() | ![]() Title: Structure and catalytic mechanism of the evolutionarily unique bacterial chalcone isomerase. Authors: Maren Thomsen / Anne Tuukkanen / Jonathan Dickerhoff / Gottfried J Palm / Hanna Kratzat / Dmitri I Svergun / Klaus Weisz / Uwe T Bornscheuer / Winfried Hinrichs / ![]() 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. #1: Journal: Arch.Microbiol. / Year: 2004 Title: First Bacterial Chalcone Isomerase Isolated from Eubacterium Ramulus. Authors: Herles, C. / Braune, A. / Blaut, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 699.6 KB | Display | ![]() |
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PDB format | ![]() | 608.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 491.7 KB | Display | ![]() |
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Full document | ![]() | 502.2 KB | Display | |
Data in XML | ![]() | 78.6 KB | Display | |
Data in CIF | ![]() | 117.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 32828.789 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | Sequence details | GENBANK KF154734 | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.88 Å3/Da / Density % sol: 74.8 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.1 M HEPES PH 7.5, 0.2 M SODIUM CHLORIDE, 1.3 M AMMONIUM SULFATE; CRYO: 0.1 M HEPES PH 7.5, 0.2 M SODIUM CHLORIDE, 2 M AMMONIUM SULFATE, 22% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 28, 2012 / Details: MIRROR |
Radiation | Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 457839 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 7.72 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 11.41 |
Reflection shell | Resolution: 1.98→2.1 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.2 / Mean I/σ(I) obs: 1.75 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 1.98→48.45 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 4.148 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.466 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→48.45 Å
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Refine LS restraints |
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