7YC4 | pdb_00007yc4

Acetylesterase (LgEstI) F207A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.245 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.198 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7YC4

This is version 1.1 of the entry. See complete history

Literature

Crystal structure and biochemical analysis of acetylesterase (LgEstI) from Lactococcus garvieae.

Do, H.Yoo, W.Wang, Y.Nam, Y.Shin, S.C.Kim, H.W.Kim, K.K.Lee, J.H.

(2023) PLoS One 18: e0280988-e0280988

  • DOI: https://doi.org/10.1371/journal.pone.0280988
  • Primary Citation Related Structures: 
    7YC0, 7YC4

  • PubMed Abstract: 

    Esterase, a member of the serine hydrolase family, catalyzes the cleavage and formation of ester bonds with high regio- and stereospecificity, making them attractive biocatalysts for the synthesis of optically pure molecules. In this study, we performed an in-depth biochemical and structural characterization of a novel microbial acetylesterase, LgEstI, from the bacterial fish pathogen Lactococcus garvieae. The dimeric LgEstI displayed substrate preference for the short acyl chain of p-nitrophenyl esters and exhibited increased activity with F207A mutation. Comparative analysis with other esterases indicated that LgEstI has a narrow and shallow active site that may exhibit substrate specificity to short acyl chains. Unlike other esterases, LgEstI contains bulky residues such as Trp89, Phe194, and Trp217, which block the acyl chain channel. Furthermore, immobilized LgEstI retained approximately 90% of its initial activity, indicating its potential in industrial applications. This study expands our understanding of LgEstI and proposes novel ideas for improving its catalytic efficiency and substrate specificity for various applications.


  • Organizational Affiliation
    • Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, Korea.

Macromolecule Content 

  • Total Structure Weight: 290.18 kDa 
  • Atom Count: 20,717 
  • Modeled Residue Count: 2,519 
  • Deposited Residue Count: 2,560 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha/beta hydrolase
A, B, C, D, E
A, B, C, D, E, F, G, H
320Lactococcus garvieae subsp. garvieaeMutation(s): 1 
Gene Names: F4V47_03290
UniProt
Find proteins for A0AA82WP15 (Lactococcus garvieae subsp. garvieae)
Explore A0AA82WP15 
Go to UniProtKB:  A0AA82WP15
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AA82WP15
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.245 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.198 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.2α = 90
b = 127.39β = 90.173
c = 104.76γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2021M1A5A1075524

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-07
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description