+Open data
-Basic information
Entry | Database: PDB / ID: 4d06 | ||||||
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Title | Bacterial chalcone isomerase complexed with naringenin | ||||||
Components | CHALCONE ISOMERASE | ||||||
Keywords | ISOMERASE / BACTERIAL CHALCONE ISOMERASE / FLAVONOIDS / NARINGENIN | ||||||
Function / homology | Chalcone isomerase, N-terminal / Chalcone isomerase N-terminal domain / chalcone isomerase / chalcone isomerase activity / NARINGENIN / Chem-X8W / Chalcone isomerase Function and homology information | ||||||
Biological species | EUBACTERIUM RAMULUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Thomsen, M. / Palm, G.J. / Hinrichs, W. | ||||||
Citation | Journal: Acta Crystallogr D Biol Crystallogr / Year: 2015 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4d06.cif.gz | 722.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d06.ent.gz | 606 KB | Display | PDB format |
PDBx/mmJSON format | 4d06.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4d06_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 4d06_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 4d06_validation.xml.gz | 83.5 KB | Display | |
Data in CIF | 4d06_validation.cif.gz | 121.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/4d06 ftp://data.pdbj.org/pub/pdb/validation_reports/d0/4d06 | HTTPS FTP |
-Related structure data
Related structure data | 4c9sSC 4c9tC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 32537.928 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) EUBACTERIUM RAMULUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: V9P0A9, chalcone isomerase |
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-Non-polymers , 5 types, 1923 molecules
#2: Chemical | ChemComp-NAR / #3: Chemical | ChemComp-CL / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.47 Å3/Da / Density % sol: 72.5 % Description: DATA WERE PROCESSED WITH FRIEDEL'S LAW - FALSE. |
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Crystal grow | pH: 7.5 Details: 0.1 M HEPES PH 7.5, 0.2 M SODIUM CHLORIDE, 1.6 M AMMONIUM SULFATE, 380 MIKROM NARINGENIN CHALCONE DISSOLVED IN ETHANOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9785 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2013 / Details: MIRROR |
Radiation | Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 436945 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.94 |
Reflection shell | Resolution: 2→2.12 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.9 / % possible all: 98.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4C9S Resolution: 2→49.18 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 5.809 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.09 / 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: 24.527 Å2
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Refinement step | Cycle: LAST / Resolution: 2→49.18 Å
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