Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48.18 kDa 
• Atom Count: 3729 
• Modelled Residue Count: 416 
• Deposited Residue Count: 446 
• Unique protein chains: 1

5WL6

Crystal structure of chalcone isomerase engineered from ancestral inference (AncR7)

• PDB DOI: 10.2210/pdb5WL6/pdb

• Classification: ISOMERASE
• Organism(s): unidentified
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2017-07-25 Released: 2018-05-09 
• Deposition Author(s): Burke, J.R., Kaltenbach, M., Tawfik, D.S., Noel, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.212 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 

Literature

Evolution of chalcone isomerase from a noncatalytic ancestor.

Kaltenbach, M., Burke, J.R., Dindo, M., Pabis, A., Munsberg, F.S., Rabin, A., Kamerlin, S.C.L., Noel, J.P., Tawfik, D.S.

(2018) Nat Chem Biol 14: 548-555

• PubMed: 29686356 
• DOI: 10.1038/s41589-018-0042-3
• Primary Citation of Related Structures:  
  5WKR, 5WKS, 5WL3, 5WL4, 5WL5, 5WL6, 5WL7, 5WL8


• PubMed Abstract: 
  

The emergence of catalysis in a noncatalytic protein scaffold is a rare, unexplored event. Chalcone isomerase (CHI), a key enzyme in plant flavonoid biosynthesis, is presumed to have evolved from a nonenzymatic ancestor related to the widely distributed fatty-acid binding proteins (FAPs) and a plant protein family with no isomerase activity (CHILs). Ancestral inference supported the evolution of CHI from a protein lacking isomerase activity. Further, we identified four alternative founder mutations, i.e., mutations that individually instated activity, including a mutation that is not phylogenetically traceable. Despite strong epistasis in other cases of protein evolution, CHI's laboratory reconstructed mutational trajectory shows weak epistasis. Thus, enantioselective CHI activity could readily emerge despite a catalytically inactive starting point. Accordingly, X-ray crystallography, NMR, and molecular dynamics simulations reveal reshaping of the active site toward a productive substrate-binding mode and repositioning of the catalytic arginine that was inherited from the ancestral fatty-acid binding proteins.

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Organizational Affiliation: 

Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Engineered Chalcone Isomerase AncR7	A, B	223	unidentified	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth B], E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.212 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.18	α = 98.68
b = 49.57	β = 92.02
c = 63.1	γ = 107.9

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-07-25 
• Released Date: 2018-05-09 
Deposition Author(s): Burke, J.R., Kaltenbach, M., Tawfik, D.S., Noel, J.P.

Revision History  

• Version 1.0: 2018-05-09
  Type: Initial release
  
• Version 1.1: 2018-05-30
  Changes: Data collection, Database references