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- PDB-4d06: Bacterial chalcone isomerase complexed with naringenin -

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Basic information

Entry
Database: PDB / ID: 4d06
TitleBacterial chalcone isomerase complexed with naringenin
ComponentsCHALCONE ISOMERASE
KeywordsISOMERASE / BACTERIAL CHALCONE ISOMERASE / FLAVONOIDS / NARINGENIN
Function / homologyChalcone isomerase, N-terminal / Chalcone isomerase N-terminal domain / chalcone isomerase / chalcone isomerase activity / NARINGENIN / Chem-X8W / Chalcone isomerase
Function and homology information
Biological speciesEUBACTERIUM RAMULUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsThomsen, M. / Palm, G.J. / Hinrichs, W.
CitationJournal: 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
DepositionApr 24, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHALCONE ISOMERASE
B: CHALCONE ISOMERASE
C: CHALCONE ISOMERASE
D: CHALCONE ISOMERASE
E: CHALCONE ISOMERASE
F: CHALCONE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,46534
Polymers195,2286
Non-polymers3,23728
Water34,1381895
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34430 Å2
ΔGint-293 kcal/mol
Surface area52840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.165, 187.991, 196.221
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11D-302-

NAR

21D-302-

NAR

31D-302-

NAR

41D-302-

NAR

51E-403-

CL

61F-301-

NAR

71F-301-

NAR

81D-2273-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.42472, 0.24444, -0.8717), (0.2511, -0.89328, -0.37283), (-0.86981, -0.37723, 0.31802)171.64499, 219.35017, 175.83125
2given(0.05184, 0.02528, 0.99834), (0.99816, -0.03274, -0.051), (0.0314, 0.99914, -0.02693)80.43002, 9.46598, -96.32295
3given(0.20383, -0.88725, -0.4138), (-0.88595, -0.34703, 0.30768), (-0.41659, 0.30389, -0.8568)222.34276, 267.84393, 72.77539
4given(0.05354, 0.99796, 0.03466), (0.01534, -0.03553, 0.99925), (0.99845, -0.05296, -0.01721)-10.85802, 96.11359, -82.65588
5given(-0.88653, -0.38977, 0.2493), (-0.38041, 0.30734, -0.87225), (0.26335, -0.86811, -0.42074)271.6524, 161.91174, 122.73074

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
CHALCONE ISOMERASE /


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 / NARINGENIN / Naringenin


Mass: 272.253 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C15H12O5
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-X8W / (2E)-3-(4-hydroxyphenyl)-1-(2,4,6-trihydroxyphenyl)prop-2-en-1-one / NARINGENIN CHALCONE / Naringenin chalcone


Mass: 272.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12O5
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1895 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.47 Å3/Da / Density % sol: 72.5 %
Description: DATA WERE PROCESSED WITH FRIEDEL'S LAW - FALSE.
Crystal growpH: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9785
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2013 / Details: MIRROR
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2→2.12 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.9 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C9S

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.
RfactorNum. reflection% reflectionSelection details
Rfree0.16277 11215 5 %RANDOM
Rwork0.14023 ---
obs0.14136 213076 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.527 Å2
Baniso -1Baniso -2Baniso -3
1-3.34 Å20 Å20 Å2
2---0.53 Å20 Å2
3----2.81 Å2
Refinement stepCycle: LAST / Resolution: 2→49.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13242 0 197 1895 15334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0214168
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212936
X-RAY DIFFRACTIONr_angle_refined_deg1.9381.95719343
X-RAY DIFFRACTIONr_angle_other_deg0.994329896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.73651699
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49324.176692
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.025152272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7961569
X-RAY DIFFRACTIONr_chiral_restr0.1210.21945
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02116091
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023410
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0210.6766575
X-RAY DIFFRACTIONr_mcbond_other1.0210.6766574
X-RAY DIFFRACTIONr_mcangle_it1.6861.0068227
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4930.7727593
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.998→2.049 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 803 -
Rwork0.267 15254 -
obs--97.57 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.09910.00970.0390.1535-0.05130.1687-0.0354-0.02550.04280.05770.03060.0138-0.00050.00630.00480.05340.04260.00440.2466-0.01720.293118.74130.659.583
20.3117-0.0269-0.00440.09030.03150.0564-0.0367-0.015-0.02090.02610.02940.05010.01890.02630.00730.02910.01990.03890.22190.02060.3305100.01111.01841.969
30.1365-0.0820.00150.15790.03580.1207-0.00490.01940.06160.01610.0026-0.0273-0.00980.03150.00230.0042-0.0059-0.01410.22340.00660.3735127.876152.83527.697
40.1712-0.01950.02660.0317-0.00050.2643-0.0050.04280.02010.0172-0.01150.00570.0014-0.01340.01650.01030.00860.00380.25360.01340.3475106.768135.44110.352
50.21570.0385-0.09320.1239-0.00250.1735-0.0344-0.0180.01680.02970.0053-0.02960.03270.06240.02910.01960.0298-0.02210.28670.01360.3284149.845120.4336.426
60.0489-0.00580.01280.2774-0.01790.1074-0.02190.01030.0259-0.0082-0.0017-0.00740.04590.01540.02350.03860.02330.02140.24830.00610.3116130.82103.21316.542
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 105
2X-RAY DIFFRACTION1A106 - 130
3X-RAY DIFFRACTION1A131 - 282
4X-RAY DIFFRACTION1A300 - 500
5X-RAY DIFFRACTION2B1 - 105
6X-RAY DIFFRACTION2B106 - 130
7X-RAY DIFFRACTION2B131 - 282
8X-RAY DIFFRACTION2B300 - 500
9X-RAY DIFFRACTION3C1 - 105
10X-RAY DIFFRACTION3C106 - 130
11X-RAY DIFFRACTION3C131 - 282
12X-RAY DIFFRACTION3C300 - 500
13X-RAY DIFFRACTION4D1 - 105
14X-RAY DIFFRACTION4D106 - 130
15X-RAY DIFFRACTION4D131 - 282
16X-RAY DIFFRACTION4D300 - 500
17X-RAY DIFFRACTION5E1 - 105
18X-RAY DIFFRACTION5E106 - 130
19X-RAY DIFFRACTION5E131 - 282
20X-RAY DIFFRACTION5E300 - 500
21X-RAY DIFFRACTION6F1 - 105
22X-RAY DIFFRACTION6F106 - 130
23X-RAY DIFFRACTION6F131 - 282
24X-RAY DIFFRACTION6F300 - 500

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