structure of lipase mutant with Cys-His-Asp catalytic triad

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Artificial cysteine-lipases with high activity and altered catalytic mechanism created by laboratory evolution.

Cen, Y.Singh, W.Arkin, M.Moody, T.S.Huang, M.Zhou, J.Wu, Q.Reetz, M.T.

(2019) Nat Commun 10: 3198-3198

  • DOI: https://doi.org/10.1038/s41467-019-11155-3
  • Primary Citation of Related Structures:  
    6ISP, 6ISQ, 6ISR

  • PubMed Abstract: 

    Engineering artificial enzymes with high activity and catalytic mechanism different from naturally occurring enzymes is a challenge in protein design. For example, many attempts have been made to obtain active hydrolases by introducing a Ser → Cys exchange at the respective catalytic triads, but this generally induced a breakdown of activity. We now report that this long-standing dogma no longer pertains, provided additional mutations are introduced by directed evolution. By employing Candida antarctica lipase B (CALB) as the model enzyme with the Ser-His-Asp catalytic triad, a highly active cysteine-lipase having a Cys-His-Asp catalytic triad and additional mutations W104V/A281Y/A282Y/V149G can be evolved, showing a 40-fold higher catalytic efficiency than wild-type CALB in the hydrolysis of 4-nitrophenyl benzoate, and tolerating bulky substrates. Crystal structures, kinetics, MD simulations and QM/MM calculations reveal dynamic features and explain all results, including the preference of a two-step mechanism involving the zwitterionic pair Cys105 - /His224 + rather than a concerted process.

  • Organizational Affiliation

    Department of Chemistry, Zhejiang University, 310027, Hangzhou, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lipase B
A, B
321Moesziomyces antarcticusMutation(s): 7 
Membrane Entity: Yes 
Find proteins for P41365 (Pseudozyma antarctica)
Explore P41365 
Go to UniProtKB:  P41365
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41365
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.288α = 90
b = 44.559β = 89.41
c = 132.947γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-08-07
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description