3WJ1

Crystal structure of SSHESTI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insights into the low pH adaptation of a unique carboxylesterase from Ferroplasma: altering the pH optima of two carboxylesterases.

Ohara, K.Unno, H.Oshima, Y.Hosoya, M.Fujino, N.Hirooka, K.Takahashi, S.Yamashita, S.Kusunoki, M.Nakayama, T.

(2014) J.Biol.Chem. 289: 24499-24510

  • DOI: 10.1074/jbc.M113.521856
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • To investigate the mechanism for low pH adaptation by a carboxylesterase, structural and biochemical analyses of EstFa_R (a recombinant, slightly acidophilic carboxylesterase from Ferroplasma acidiphilum) and SshEstI (an alkaliphilic carboxylesterase ...

    To investigate the mechanism for low pH adaptation by a carboxylesterase, structural and biochemical analyses of EstFa_R (a recombinant, slightly acidophilic carboxylesterase from Ferroplasma acidiphilum) and SshEstI (an alkaliphilic carboxylesterase from Sulfolobus shibatae DSM5389) were performed. Although a previous proteomics study by another group showed that the enzyme purified from F. acidiphilum contained an iron atom, EstFa_R did not bind to iron as analyzed by inductively coupled plasma MS and isothermal titration calorimetry. The crystal structures of EstFa_R and SshEstI were determined at 1.6- and 1.5-Å resolutions, respectively. EstFa_R had a catalytic triad with an extended hydrogen bond network that was not observed in SshEstI. Quadruple mutants of both proteins were created to remove or introduce the extended hydrogen bond network. The mutation on EstFa_R enhanced its catalytic efficiency and gave it an alkaline pH optimum, whereas the mutation on SshEstI resulted in opposite effects (i.e. a decrease in the catalytic efficiency and a downward shift in the optimum pH). Our experimental results suggest that the low pH optimum of EstFa_R activity was a result of the unique extended hydrogen bond network in the catalytic triad and the highly negatively charged surface around the active site. The change in the pH optimum of EstFa_R happened simultaneously with a change in the catalytic efficiency, suggesting that the local flexibility of the active site in EstFa_R could be modified by quadruple mutation. These observations may provide a novel strategy to elucidate the low pH adaptation of serine hydrolases.


    Organizational Affiliation

    From the Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-11, Sendai 980-8579, Japan, satoshi0207@gmail.com.,Faculty of Life and Environmental Sciences, University of Yamanashi, 4-3-37 Takeda, Kofu 400-8511, Japan.,Graduate School of Engineering, Nagasaki University, Bunkyo-machi 1-14, Nagasaki 852-8521, Japan, and.,From the Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-11, Sendai 980-8579, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carboxylesterase
A
305Saccharolobus shibataeMutation(s): 0 
Gene Names: SshEstI
Find proteins for Q5NU42 (Saccharolobus shibatae)
Go to UniProtKB:  Q5NU42
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BOG
Query on BOG

Download SDF File 
Download CCD File 
A
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.157 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 58.403α = 90.00
b = 71.942β = 90.00
c = 137.332γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2019-12-25
    Type: Database references, Derived calculations