3ZPH | pdb_00003zph

Bacterial chalcone isomerase in closed conformation from Eubacterium ramulus at 2.8 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.297 (Depositor), 0.292 (DCC) 
  • R-Value Work: 
    0.248 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.250 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3ZPH

This is version 1.4 of the entry. See complete history

Literature

Enzymatic conversion of flavonoids using bacterial chalcone isomerase and enoate reductase.

Gall, M.Thomsen, M.Peters, C.Pavlidis, I.V.Jonczyk, P.Grunert, P.P.Beutel, S.Scheper, T.Gross, E.Backes, M.Geissler, T.Ley, J.P.Hilmer, J.M.Krammer, G.Palm, G.J.Hinrichs, W.Bornscheuer, U.T.

(2014) Angew Chem Int Ed Engl 53: 1439-1442

  • DOI: https://doi.org/10.1002/anie.201306952
  • Primary Citation Related Structures: 
    3ZPH

  • PubMed Abstract: 

    Flavonoids are a large group of plant secondary metabolites with a variety of biological properties and are therefore of interest to many scientists, as they can lead to industrially interesting intermediates. The anaerobic gut bacterium Eubacterium ramulus can catabolize flavonoids, but until now, the pathway has not been experimentally confirmed. In the present work, a chalcone isomerase (CHI) and an enoate reductase (ERED) could be identified through whole genome sequencing and gene motif search. These two enzymes were successfully cloned and expressed in Escherichia coli in their active form, even under aerobic conditions. The catabolic pathway of E. ramulus was confirmed by biotransformations of flavanones into dihydrochalcones. The engineered E. coli strain that expresses both enzymes was used for the conversion of several flavanones, underlining the applicability of this biocatalytic cascade reaction.


  • Organizational Affiliation
    • Institute of Biochemistry, Department of Biotechnology & Enzyme Catalysis, Greifswald University, Felix-Hausdorff-Strasse 4, 17487 Greifswald (Germany) http://biotech.uni-greifswald.de.

Macromolecule Content 

  • Total Structure Weight: 195.04 kDa 
  • Atom Count: 14,021 
  • Modeled Residue Count: 1,574 
  • Deposited Residue Count: 1,692 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CHALCONE ISOMERASE
A, B, C, D, E
A, B, C, D, E, F
282Eubacterium ramulusMutation(s): 0 
EC: 5.5.1.6
UniProt
Find proteins for U2Q8X2 (Eubacterium ramulus ATCC 29099)
Explore U2Q8X2 
Go to UniProtKB:  U2Q8X2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupU2Q8X2
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
G [auth A],
J [auth C],
L [auth D],
M [auth E],
O [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
H [auth A],
I [auth B],
K [auth C],
N [auth E]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.297 (Depositor), 0.292 (DCC) 
  • R-Value Work:  0.248 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.250 (Depositor) 
Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 177.73α = 90
b = 203.12β = 90
c = 206.11γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-15
    Type: Initial release
  • Version 1.1: 2014-02-05
    Changes: Database references
  • Version 1.2: 2015-03-25
    Changes: Database references
  • Version 1.3: 2019-09-18
    Changes: Data collection, Database references
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description