Highly active enzymes by automated modular backbone assembly and sequence design

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

Starting Model: experimental
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This is version 2.0 of the entry. See complete history


Highly active enzymes by automated combinatorial backbone assembly and sequence design.

Lapidoth, G.Khersonsky, O.Lipsh, R.Dym, O.Albeck, S.Rogotner, S.Fleishman, S.J.

(2018) Nat Commun 9: 2780-2780

  • DOI: https://doi.org/10.1038/s41467-018-05205-5
  • Primary Citation of Related Structures:  
    6FHE, 6FHF

  • PubMed Abstract: 

    Automated design of enzymes with wild-type-like catalytic properties has been a long-standing but elusive goal. Here, we present a general, automated method for enzyme design through combinatorial backbone assembly. Starting from a set of homologous yet structurally diverse enzyme structures, the method assembles new backbone combinations and uses Rosetta to optimize the amino acid sequence, while conserving key catalytic residues. We apply this method to two unrelated enzyme families with TIM-barrel folds, glycoside hydrolase 10 (GH10) xylanases and phosphotriesterase-like lactonases (PLLs), designing 43 and 34 proteins, respectively. Twenty-one GH10 and seven PLL designs are active, including designs derived from templates with <25% sequence identity. Moreover, four designs are as active as natural enzymes in these families. Atomic accuracy in a high-activity GH10 design is further confirmed by crystallographic analysis. Thus, combinatorial-backbone assembly and design may be used to generate stable, active, and structurally diverse enzymes with altered selectivity or activity.

  • Organizational Affiliation

    Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Design362Escherichia coliMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.969α = 90
b = 128.969β = 90
c = 51.71γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2018-08-01
    Changes: Data collection, Database references
  • Version 2.0: 2024-01-17
    Changes: Atomic model, Data collection, Database references, Refinement description