4D06

Bacterial chalcone isomerase complexed with naringenin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.141 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

Structure and Catalytic Mechanism of the Evolutionarily Unique Bacterial Chalcone Isomerase

Thomsen, M., Tuukkanen, A., Dickerhoff, J., Palm, G.J., Kratzat, H., Svergun, D.I., Weisz, K., Bornscheuer, U.T., Hinrichs, W.

(2015) Acta Crystallogr D Biol Crystallogr 71: 907

  • DOI: 10.1107/S1399004715001935
  • Primary Citation of Related Structures:  
    4C9S, 4C9T, 4D06

  • 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 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 ...

    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.

    Organizational Affiliation: 

    Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CHALCONE ISOMERASE
A, B, C, D, E, F
A, B, C, D, E, F
283Eubacterium ramulusMutation(s): 0 
Gene Names: tai
EC: 5.5.1.6
UniProt
Find proteins for V9P0A9 (Eubacterium ramulus)
Explore V9P0A9 
Go to UniProtKB:  V9P0A9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV9P0A9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
X8W
Query on X8W
Download Ideal Coordinates CCD File 
J [auth B],
T [auth D]		(2E)-3-(4-hydroxyphenyl)-1-(2,4,6-trihydroxyphenyl)prop-2-en-1-one
C15 H12 O5
YQHMWTPYORBCMF-UHFFFAOYSA-N		 Ligand Interaction
NAR
Query on NAR
Download Ideal Coordinates CCD File 
CA [auth F],
DA [auth F],
G [auth A],
N [auth C],
R [auth D],
CA [auth F],
DA [auth F],
G [auth A],
N [auth C],
R [auth D],
S [auth D],
X [auth E]
NARINGENIN
C15 H12 O5
FTVWIRXFELQLPI-ZDUSSCGKSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
EA [auth F],
K [auth B]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
AA [auth E],
BA [auth E],
FA [auth F],
GA [auth F],
H [auth A],
AA [auth E],
BA [auth E],
FA [auth F],
GA [auth F],
H [auth A],
HA [auth F],
I [auth A],
L [auth B],
M [auth B],
O [auth C],
P [auth C],
Q [auth C],
U [auth D],
V [auth D],
W [auth D],
Y [auth E],
Z [auth E]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.141 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.165α = 90
b = 187.991β = 90
c = 196.221γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2015-04-22
    Changes: Database references