Crystal structure of PsEst3 complexed with Phenylmethylsulfonyl fluoride (PMSF)

Experimental Data Snapshot

  • Resolution: 2.34 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 

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This is version 1.2 of the entry. See complete history


Structural and biochemical insights into PsEst3, a new GHSR-type esterase obtained from Paenibacillus sp. R4.

Son, J.Choi, W.Kim, H.Kim, M.Lee, J.H.Shin, S.C.Kim, H.W.

(2023) IUCrJ 10: 220-232

  • DOI: https://doi.org/10.1107/S2052252523001562
  • Primary Citation of Related Structures:  
    7V8U, 7V8V, 7V8W, 7V8X

  • PubMed Abstract: 

    PsEst3, a psychrophilic esterase obtained from Paenibacillus sp. R4, which was isolated from the permafrost of Alaska, exhibits relatively high activity at low temperatures. Here, crystal structures of PsEst3 complexed with various ligands were generated and studied at atomic resolution, and biochemical studies were performed to analyze the structure-function relationship of PsEst3. Certain unique characteristics of PsEst3 distinct from those of other classes of lipases/esterases were identified. Firstly, PsEst3 contains a conserved GHSRA/G pentapeptide sequence in the GxSxG motif around the nucleophilic serine. Additionally, it contains a conserved HGFR/K consensus sequence in the oxyanion hole, which is distinct from that in other lipase/esterase families, as well as a specific domain composition (for example a helix-turn-helix motif) and a degenerative lid domain that exposes the active site to the solvent. Secondly, the electrostatic potential of the active site in PsEst3 is positive, which may cause unintended binding of negatively charged chemicals in the active site. Thirdly, the last residue of the oxyanion hole-forming sequence, Arg44, separates the active site from the solvent by sealing the acyl-binding pocket, suggesting that PsEst3 is an enzyme that is customized to sense an unidentified substrate that is distinct from those of classical lipases/esterases. Collectively, this evidence strongly suggests that PsEst3 belongs to a distinct family of esterases.

  • Organizational Affiliation

    Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
esterase265Paenibacillus sp.Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PMS (Subject of Investigation/LOI)
Query on PMS

Download Ideal Coordinates CCD File 
B [auth A]phenylmethanesulfonic acid
C7 H8 O3 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.34 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 
  • Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.773α = 90
b = 144.773β = 90
c = 144.773γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of2021M1A5A1075524

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-31
    Type: Initial release
  • Version 1.1: 2023-03-15
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description