5AGY

CRYSTAL STRUCTURE OF A TAU CLASS GST MUTANT FROM GLYCINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Directed Evolution of Tau Class Glutathione Transferases Reveals a Site that Regulates Catalytic Efficiency and Masks Cooperativity.

Axarli, I.Muleta, A.W.Vlachakis, D.Kossida, S.Kotzia, G.Maltezos, A.Dhavala, P.Papageorgiou, A.C.Labrou, N.E.

(2016) Biochem J 473: 559

  • DOI: https://doi.org/10.1042/BJ20150930
  • Primary Citation of Related Structures:  
    5AGY

  • PubMed Abstract: 

    A library of Tau class GSTs (glutathione transferases) was constructed by DNA shuffling using the DNA encoding the Glycine max GSTs GmGSTU2-2, GmGSTU4-4 and GmGSTU10-10. The parental GSTs are >88% identical at the sequence level; however, their specificity varies towards different substrates. The DNA library contained chimaeric structures of alternated segments of the parental sequences and point mutations. Chimaeric GST sequences were expressed in Escherichia coli and their enzymatic activities towards CDNB (1-chloro-2,4-dinitrobenzene) and the herbicide fluorodifen (4-nitrophenyl α,α,α-trifluoro-2-nitro-p-tolyl ether) were determined. A chimaeric clone (Sh14) with enhanced CDNB- and fluorodifen-detoxifying activities, and unusual co-operative kinetics towards CDNB and fluorodifen, but not towards GSH, was identified. The structure of Sh14 was determined at 1.75 Å (1 Å=0.1 nm) resolution in complex with S-(p-nitrobenzyl)-glutathione. Analysis of the Sh14 structure showed that a W114C point mutation is responsible for the altered kinetic properties. This was confirmed by the kinetic properties of the Sh14 C114W mutant. It is suggested that the replacement of the bulky tryptophan residue by a smaller amino acid (cysteine) results in conformational changes of the active-site cavity, leading to enhanced catalytic activity of Sh14. Moreover, the structural changes allow the strengthening of the two salt bridges between Glu(66) and Lys(104) at the dimer interface that triggers an allosteric effect and the communication between the hydrophobic sites.


  • Organizational Affiliation

    Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, 75 Iera Odos Street, GR-11855 Athens, Greece.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GLUTATHIONE S-TRANSFERASE
A, B
219Glycine maxMutation(s): 4 
EC: 2.5.1.18
UniProt
Find proteins for I1MJ34 (Glycine max)
Explore I1MJ34 
Go to UniProtKB:  I1MJ34
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI1MJ34
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTB
Query on GTB

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B]
S-(P-NITROBENZYL)GLUTATHIONE
C17 H22 N4 O8 S
OAWORKDPTSAMBZ-STQMWFEESA-N
4NM
Query on 4NM

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
H [auth B]
4-NITROPHENYL METHANETHIOL
C7 H8 N O2 S
OTHKGVFNUSHUQO-UHFFFAOYSA-O
PO4
Query on PO4

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.241α = 90
b = 77.602β = 90
c = 99.078γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-16
    Type: Initial release
  • Version 1.1: 2016-03-09
    Changes: Database references
  • Version 1.2: 2019-07-17
    Changes: Data collection
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description