6TY6

Variant W229D/F290W-2 of the last common ancestor of Gram-negative bacteria beta-lactamase class A (GNCA4) bound to 5(6)-nitrobenzotriazole (TS-analog)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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


Literature

Enhancing ade novoenzyme activity by computationally-focused ultra-low-throughput screening.

Risso, V.A., Romero-Rivera, A., Gutierrez-Rus, L.I., Ortega-Munoz, M., Santoyo-Gonzalez, F., Gavira, J.A., Sanchez-Ruiz, J.M., Kamerlin, S.C.L.

(2020) Chem Sci 11: 6134-6148

  • DOI: https://doi.org/10.1039/d0sc01935f
  • Primary Citation of Related Structures:  
    6TWW, 6TXD, 6TY6

  • PubMed Abstract: 

    • Directed evolution has revolutionized protein engineering. Still, enzyme optimization by random library screening remains sluggish, in large part due to futile probing of mutations that are catalytically neutral and/or impair stability and folding. FuncLib is a novel approach which uses phylogenetic analysis and Rosetta design to rank enzyme variants with multiple mutations, on the basis of predicted stability ...

    Directed evolution has revolutionized protein engineering. Still, enzyme optimization by random library screening remains sluggish, in large part due to futile probing of mutations that are catalytically neutral and/or impair stability and folding. FuncLib is a novel approach which uses phylogenetic analysis and Rosetta design to rank enzyme variants with multiple mutations, on the basis of predicted stability. Here, we use it to target the active site region of a minimalist-designed, de novo Kemp eliminase. The similarity between the Michaelis complex and transition state for the enzymatic reaction makes this system particularly challenging to optimize. Yet, experimental screening of a small number of active-site variants at the top of the predicted stability ranking leads to catalytic efficiencies and turnover numbers (∼2 × 10 4 M -1 s -1 and ∼10 2 s -1 ) for this anthropogenic reaction that compare favorably to those of modern natural enzymes. This result illustrates the promise of FuncLib as a powerful tool with which to speed up directed evolution, even on scaffolds that were not originally evolved for those functions, by guiding screening to regions of the sequence space that encode stable and catalytically diverse enzymes. Empirical valence bond calculations reproduce the experimental activation energies for the optimized eliminases to within ∼2 kcal mol -1 and indicate that the enhanced activity is linked to better geometric preorganization of the active site. This raises the possibility of further enhancing the stability-guidance of FuncLib by computational predictions of catalytic activity, as a generalized approach for computational enzyme design.

    Organizational Affiliation: 

    Science for Life Laboratory , Department of Chemistry-BMC , Uppsala University , BMC Box 576 , S-751 23 Uppsala , Sweden . Email: lynn.kamerlin@kemi.uu.se.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta lactamase (GNCA4-2)A, B, C269synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6NT (Subject of Investigation/LOI)
Query on 6NT
Download Ideal Coordinates CCD File 
AA [auth B],
HA [auth C],
N [auth A]		6-NITROBENZOTRIAZOLE
C6 H4 N4 O2
AOCDQWRMYHJTMY-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
BA [auth C],
D [auth A],
J [auth A],
P [auth B],
U [auth B]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
ACT
Query on ACT
Download Ideal Coordinates CCD File 
G [auth A],
GA [auth C],
H [auth A],
L [auth A],
V [auth B]		ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
FMT
Query on FMT
Download Ideal Coordinates CCD File 
CA [auth C],
DA [auth C],
E [auth A],
EA [auth C],
F [auth A],
CA [auth C],
DA [auth C],
E [auth A],
EA [auth C],
F [auth A],
FA [auth C],
I [auth A],
K [auth A],
O [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
M [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.384α = 90
b = 148.357β = 90
c = 246.008γ = 90
Software Package:
Software NamePurpose
EDNAdata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainBIO2016-74875-P
Spanish Ministry of Economy and CompetitivenessSpainBIO2015-66426-R
Human Frontier Science Program (HFSP)United StatesRGP0041/2017

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-03
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Database references