1GSQ

THREE-DIMENSIONAL STRUCTURE, CATALYTIC PROPERTIES AND EVOLUTION OF A SIGMA CLASS GLUTATHIONE TRANSFERASE FROM SQUID, A PROGENITOR OF THE LENS-CRYSTALLINS OF CEPHALOPODS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Three-dimensional structure, catalytic properties, and evolution of a sigma class glutathione transferase from squid, a progenitor of the lens S-crystallins of cephalopods.

Ji, X.von Rosenvinge, E.C.Johnson, W.W.Tomarev, S.I.Piatigorsky, J.Armstrong, R.N.Gilliland, G.L.

(1995) Biochemistry 34: 5317-5328

  • DOI: https://doi.org/10.1021/bi00016a003
  • Primary Citation of Related Structures:  
    1GSQ

  • PubMed Abstract: 

    The glutathione transferase from squid digestive gland is unique in its very high catalytic activity toward 1-chloro-2,4-dinitrobenzene and in its ancestral relationship to the genes encoding the S-crystallins of the lens of cephalopod eye. The three-dimensional structure of this glutathione transferase in complex with the product 1-(S-glutathionyl)-2,4-dinitrobenzene (GSDNB) has been solved by multiple isomorphous replacement techniques at a resolution of 2.4 A. Like the cytosolic enzymes from vertebrates, the squid protein is a dimer. The structure is similar in overall topology to the vertebrate enzymes but has a dimer interface that is unique when compared to all of the vertebrate and invertebrate structures thus far reported. The active site of the enzyme is very open, a fact that appears to correlate with the high turnover number (800 s-1 at pH 6.5) toward 1-chloro-2,4-dinitrobenzene. Both kcat and kcat/KmCDNB exhibit pH dependencies consistent with a pKa for the thiol of enzyme-bound GSH of 6.3. The enzyme is not very efficient at catalyzing the addition of GSH to enones and epoxides. This particular characteristic appears to be due to the lack of an electrophilic residue at position 106, which is often found in other GSH transferases. The F106Y mutant enzyme is much improved in catalyzing these reactions. Comparisons of the primary structure, gene structure, and three-dimensional structure with class alpha, mu, and pi enzymes support placing the squid protein in a separate enzyme class, sigma. The unique dimer interface suggests that the class sigma enzyme diverged from the ancestral precursor prior to the divergence of the precursor gene for the alpha, mu, and pi classes.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Maryland, College Park 20742, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GLUTATHIONE S-TRANSFERASE202Todarodes pacificusMutation(s): 0 
Gene Names: CDNA INSERT OF CLONE PGST5
EC: 2.5.1.18
UniProt
Find proteins for P46088 (Nototodarus sloanii)
Explore P46088 
Go to UniProtKB:  P46088
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46088
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDN
Query on GDN

Download Ideal Coordinates CCD File 
B [auth A]GLUTATHIONE S-(2,4 DINITROBENZENE)
C16 H19 N5 O10 S
FXEUKVKGTKDDIQ-UWVGGRQHSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Observed: 0.180 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.76α = 90
b = 72.76β = 90
c = 94.63γ = 120
Software Package:
Software NamePurpose
GPRLSArefinement
PROLSQrefinement
XENGENdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-06-03
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2019-07-17
    Changes: Data collection, Other, Refinement description
  • Version 1.4: 2019-08-14
    Changes: Data collection, Refinement description
  • Version 1.5: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Structure summary