Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 47578.41 
• Atom Count: 3381 
• Residue Count: 416 
• Unique protein chains: 1

1LBK

Crystal structure of a recombinant glutathione transferase, created by replacing the last seven residues of each subunit of the human class pi isoenzyme with the additional C-terminal helix of human class alpha isoenzyme

• DOI: 10.2210/pdb1LBK/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2002-04-04 Released: 2002-04-17 
• Deposition Author(s): Kong, G.K.W., Micaloni, C., Mazzetti, A.P., Nuccetelli, M., Antonini, G., Stella, L., McKinstry, W.J., Polekhina, G., Rossjohn, J., Federici, G., Ricci, G., Parker, M.W., Lo Bello, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.224 
• R-Value Work: 0.198 

Literature

Engineering a new C-terminal tail in the H-site of human glutathione transferase P1-1: structural and functional consequences.

Micaloni, C., Kong, G.K.W., Mazzetti, A.P., Nuccetelli, M., Antonini, G., Stella, L., McKinstry, W.J., Polekhina, G., Rossjohn, J., Federici, G., Ricci, G., Parker, M.W., Lo Bello, M.

(2003) J.Mol.Biol. 325: 111-122

• PubMed: 12473455 


• PubMed Abstract: 
  

We have sought the structural basis for the differing substrate specificities of human glutathione transferase P1-1 (class Pi) and human glutathione transferase A1-1 (class Alpha) by adding an extra helix (helix 9), found in the electrophilic substrate-binding site (H-site) of the human class Alpha enzyme, at the C terminus of the human class Pi enzyme. This class Pi-chimera (CODA) was expressed in Escherichia coli, purified and characterized by kinetic and crystallographic approaches. The presence of the newly engineered tail in the H-site of the human Pi enzyme alters its catalytic properties towards those exhibited by the human Alpha enzyme, as assessed using cumene hydroperoxide (diagnostic for class Alpha enzymes) and ethacrynic acid (diagnostic for class Pi) as co-substrates. There is a change of substrate selectivity in the latter case, as the k(cat)/K(m)(EA) value decreases about 70-fold, compared to that of class Pi. With 1-chloro-2,4-dinitrobenzene as co-substrate there is a loss of catalytic activity to about 2% with respect to that of the Pi enzyme. Crystallographic and kinetic studies of the class Pi-chimera provide important clues to explain these altered catalytic properties. The new helix forms many complimentary interactions with the rest of the protein and re-models the original electrophilic substrate-binding site towards one that is more enclosed, albeit flexible. Of particular note are the interactions between Glu205 of the new tail and the catalytic residues, Tyr7 and Tyr108, and the thiol moiety of glutathione (GSH). These interactions may provide an explanation of the more than one unit increase in the pK(a) value of the GSH thiolate and affect both the turnover number and GSH binding, using 1-chloro-2,4-dinitrobenzene as co-substrate. The data presented are consistent with the engineered tail adopting a highly mobile or disordered state in the apo form of the enzyme.

---

Organizational Affiliation: 

Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica snc, 00133 Rome, Italy.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Glutathione S-transferase class pi chimaera (CODA)	A, B	208	Homo sapiens	Mutation(s): 0  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GSH	A, B	GLUTATHIONE C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N
MES	A, B	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
GSH	Kd: 668000 nM BINDINGMOAD
GSH	Kd: 668000 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.224 
• R-Value Work: 0.198 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 68.300	α = 90.00
b = 79.300	β = 90.00
c = 89.900	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	refinement
DENZO	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-04-04 
• Released Date: 2002-04-17 
• Deposition Author(s): Kong, G.K.W., Micaloni, C., Mazzetti, A.P., Nuccetelli, M., Antonini, G., Stella, L., McKinstry, W.J., Polekhina, G., Rossjohn, J., Federici, G., Ricci, G., Parker, M.W., Lo Bello, M.

Revision History 

• Version 1.0: 2002-04-17
  Type: Initial release
• Version 1.1: 2008-04-28
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-08-23
  Type: Refinement description, Source and taxonomy