Marine microorganism esterase

Experimental Data Snapshot

  • Resolution: 2.03 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.200 

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This is version 1.2 of the entry. See complete history


Structural Insights into a Novel Esterase from the East Pacific Rise and Its Improved Thermostability by a Semirational Design.

Zhu, C.Chen, Y.Isupov, M.N.Littlechild, J.A.Sun, L.Liu, X.Wang, Q.Gong, H.Dong, P.Zhang, N.Wu, Y.

(2021) J Agric Food Chem 69: 1079-1090

  • DOI: https://doi.org/10.1021/acs.jafc.0c06338
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Lipolytic enzymes are essential biocatalysts in food processing as well as pharmaceutical and pesticide industries, catalyzing the cleavage of ester bonds in a variety of acyl chain substrates. Here, we report the crystal structure of an esterase from the deep-sea hydrothermal vent of the East Pacific Rise (EprEst). The X-ray structure of EprEst in complex with the ligand, acetate, has been determined at 2.03 Å resolution. The structure reveals a unique spatial arrangement and orientation of the helix cap domain and α/β hydrolase domain, which form a substrate pocket with preference for short-chain acyl groups. Molecular docking analysis further demonstrated that the active site pocket could accommodate p -nitrophenyl ( p NP) carboxyl ligands of varying lengths (≤6 C atoms), with p NP-butyrate ester predicted to have the highest binding affinity. Additionally, the semirational design was conducted to improve the thermostability of EprEst by enzyme engineering based on the established structure and multiple sequence alignment. A mutation, K114P, introduced in the hinge region of the esterase, which displayed increased thermostability and enzyme activity. Collectively, the structural and functional data obtained herein could be used as basis for further protein engineering to ultimately expand the scope of industrial applications of marine-derived lipolytic enzymes.

  • Organizational Affiliation

    State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative esterase271uncultured bacteriumMutation(s): 0 
Find proteins for A0A2S1GUX0 (uncultured bacterium)
Explore A0A2S1GUX0 
Go to UniProtKB:  A0A2S1GUX0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2S1GUX0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.03 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.200 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67α = 90
b = 67β = 90
c = 62γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
Cootmodel building
DMMultimodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-26
    Type: Initial release
  • Version 1.1: 2021-12-22
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Derived calculations, Refinement description