5RGF

Crystal Structure of Kemp Eliminase HG4 with bound transition state analogue, 277K

• PDB DOI:  https://doi.org/10.2210/pdb5RGF/pdb
• Deposition Group: G_1002148 ExploreG_1002148

• Classification: HYDROLASE
• Organism(s): Thermoascus aurantiacus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-03-19 Released: 2020-07-22 
• Deposition Author(s): Broom, A., Rakotoharisoa, R.V., Thompson, M.C., Fraser, J.S., Chica, R.A.
• Funding Organization(s): Natural Sciences and Engineering Research Council of Canada

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 0.150 
• R-Value Work: 0.132 

Literature

Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico.

Broom, A., Rakotoharisoa, R.V., Thompson, M.C., Zarifi, N., Nguyen, E., Mukhametzhanov, N., Liu, L., Fraser, J.S., Chica, R.A.

(2020) Nat Commun 11: 4808-4808

• PubMed: 32968058 
• DOI: https://doi.org/10.1038/s41467-020-18619-x
• Primary Citation of Related Structures:  
  5RG4, 5RG5, 5RG6, 5RG7, 5RG8, 5RG9, 5RGA, 5RGB, 5RGC, 5RGD, 5RGE, 5RGF


• PubMed Abstract: 
  

The creation of artificial enzymes is a key objective of computational protein design. Although de novo enzymes have been successfully designed, these exhibit low catalytic efficiencies, requiring directed evolution to improve activity. Here, we use room-temperature X-ray crystallography to study changes in the conformational ensemble during evolution of the designed Kemp eliminase HG3 (k _cat /K _M 146 M ^-1 s ^-1 ). We observe that catalytic residues are increasingly rigidified, the active site becomes better pre-organized, and its entrance is widened. Based on these observations, we engineer HG4, an efficient biocatalyst (k _cat /K _M 103,000 M ^-1 s ^-1 ) containing key first and second-shell mutations found during evolution. HG4 structures reveal that its active site is pre-organized and rigidified for efficient catalysis. Our results show how directed evolution circumvents challenges inherent to enzyme design by shifting conformational ensembles to favor catalytically-productive sub-states, and suggest improvements to the design methodology that incorporate ensemble modeling of crystallographic data.

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Organizational Affiliation: 

Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie, Ottawa, ON, K1N 6N5, Canada. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 69.28 kDa 
• Atom Count: 5,702 
• Modelled Residue Count: 602 
• Deposited Residue Count: 636 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kemp Eliminase HG3	A, B	318	Thermoascus aurantiacus	Mutation(s): 17  Gene Names: XYNA EC: 3.2.1.8
UniProt
Find proteins for P23360 (Thermoascus aurantiacus) Explore P23360  Go to UniProtKB:  P23360

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6NT (Subject of Investigation/LOI)	C [auth A], F [auth B]	6-NITROBENZOTRIAZOLE C6 H4 N4 O2 AOCDQWRMYHJTMY-UHFFFAOYSA-N
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 0.150 
• R-Value Work: 0.132 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.41	α = 90
b = 79.94	β = 90
c = 99.01	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-07-22 
Deposition Author(s): Broom, A., Rakotoharisoa, R.V., Thompson, M.C., Fraser, J.S., Chica, R.A.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council of Canada	Canada	--

Revision History  

• Version 1.0: 2020-07-22
  Type: Initial release
  
• Version 1.1: 2020-12-02
  Changes: Database references
• Version 1.2: 2021-05-12
  Changes: Structure summary