6ISR | pdb_00006isr

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

• PDB DOI: https://doi.org/10.2210/pdb6ISR/pdb

• Classification: HYDROLASE
• Organism(s): Moesziomyces antarcticus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 
• Membrane Protein: Yes  OPM


• Deposited: 2018-11-18 Released: 2019-07-24 
• Deposition Author(s): Cen, Y.X., Zhou, J.H., Wu, Q.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.228 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.179 (Depositor) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

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

• PubMed: 31324776 
• DOI: https://doi.org/10.1038/s41467-019-11155-3
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry, Zhejiang University, 310027, Hangzhou, China.
State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 200032, Shanghai, China.
School of Chemistry and Chemical Engineering, Queen's University, Belfast, Northern Ireland, BT9 5AG, UK.
Department of Biocatalysis and Isotope Chemistry, Almac Sciences, Craigavon, Northern Ireland, BT63 5QD, UK.
School of Chemistry and Chemical Engineering, Queen's University, Belfast, Northern Ireland, BT9 5AG, UK. [e-mail].
State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 200032, Shanghai, China. [e-mail].
Department of Chemistry, Zhejiang University, 310027, Hangzhou, China. [e-mail].
Max-Planck-Institut für Kohlenforschung, 45470, Mülheim an der Ruhr, Germany. [e-mail].
Chemistry Department, Philipps-University, 35032, Marburg, Germany. [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 67.71 kDa 
• Atom Count: 4,731 
• Modeled Residue Count: 628 
• Deposited Residue Count: 642 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase B	A, B	321	Moesziomyces antarcticus	Mutation(s): 7  EC: 3.1.1.3 Membrane Entity: Yes
UniProt
Find proteins for P41365 (Pseudozyma antarctica) Explore P41365  Go to UniProtKB:  P41365

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	E [auth A], I [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG	D [auth A], G [auth B], H [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
NI	C [auth A], F [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.228 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.179 (Depositor) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.288	α = 90
b = 44.559	β = 89.41
c = 132.947	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-07-24 
Deposition Author(s): Cen, Y.X., Zhou, J.H., Wu, Q.

Revision History  

• 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
• Version 1.3: 2024-10-23
  Changes: Structure summary