2J9H

Crystal structure of human glutathione-S-transferase P1-1 cys-free mutant in complex with S-hexylglutathione at 2.4 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.250 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Modulating Catalytic Activity by Unnatural Amino Acid Residues in a Gsh-Binding Loop of Gst P1-1.

Hegazy, U.M.Tars, K.Hellman, U.Mannervik, B.

(2008) J.Mol.Biol. 376: 811

  • DOI: 10.1016/j.jmb.2007.12.013

  • PubMed Abstract: 
  • The loop following helix alpha2 in glutathione transferase P1-1 has two conserved residues, Cys48 and Tyr50, important for glutathione (GSH) binding and catalytic activity. Chemical modification of Cys48 thwarts the catalytic activity of the enzyme, ...

    The loop following helix alpha2 in glutathione transferase P1-1 has two conserved residues, Cys48 and Tyr50, important for glutathione (GSH) binding and catalytic activity. Chemical modification of Cys48 thwarts the catalytic activity of the enzyme, and mutation of Tyr50 generally decreases the k(cat) value and the affinity for GSH in a differential manner. Cys48 and Tyr50 were targeted by site-specific mutations and chemical modifications in order to investigate how the alpha2 loop modulates GSH binding and catalysis. Mutation of Cys48 into Ala increased K(M)(GSH) 24-fold and decreased the binding energy of GSH by 1.5 kcal/mol. Furthermore, the protein stability against thermal inactivation and chemical denaturation decreased. The crystal structure of the Cys-free variant was determined, and its similarity to the wild-type structure suggests that the mutation of Cys48 increases the flexibility of the alpha2 loop rather than dislocating the GSH-interacting residues. On the other hand, replacement of Tyr50 with Cys, producing mutant Y50C, increased the Gibbs free energy of the catalyzed reaction by 4.8 kcal/mol, lowered the affinity for S-hexyl glutathione by 2.2 kcal/mol, and decreased the thermal stability. The targeted alkylation of Cys50 in Y50C increased the affinity for GSH and protein stability. Characterization of the most active alkylated variants, S-n-butyl-, S-n-pentyl-, and S-cyclobutylmethyl-Y50C, indicated that the affinity for GSH is restored by stabilizing the alpha2 loop through positioning of the key residue into the lock structure of the neighboring subunit. In addition, k(cat) can be further modulated by varying the structure of the key residue side chain, which impinges on the rate-limiting step of catalysis.


    Organizational Affiliation

    Department of Biochemistry and Organic Chemistry, Biomedical Center, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUTATHIONE S-TRANSFERASE P
A, B
209Homo sapiensMutation(s): 4 
Gene Names: GSTP1 (FAEES3, GST3)
EC: 2.5.1.18
Find proteins for P09211 (Homo sapiens)
Go to Gene View: GSTP1
Go to UniProtKB:  P09211
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTX
Query on GTX

Download SDF File 
Download CCD File 
A, B
S-HEXYLGLUTATHIONE
C16 H30 N3 O6 S
HXJDWCWJDCOHDG-RYUDHWBXSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GTXKi: 410000 nM BINDINGMOAD
GTXKi: 410000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.250 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 59.566α = 90.00
b = 59.566β = 90.00
c = 238.350γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
MOLREPphasing
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-14
    Type: Initial release
  • Version 1.1: 2015-09-23
    Type: Data collection, Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2018-01-17
    Type: Data collection