5G5F | pdb_00005g5f

Crystallographic structure of the Tau class glutathione S-transferase MiGSTU in complex with reduced glutathione.

• PDB DOI: https://doi.org/10.2210/pdb5G5F/pdb

• Classification: TRANSFERASE
• Organism(s): Mangifera indica
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-05-24 Released: 2017-02-01 
• Deposition Author(s): Valenzuela-Chavira, I., Serrano-Posada, H., Lopez-Zavala, A., Hernandez-Paredes, J., Sotelo-Mundo, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.243 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Insights Into Ligand Binding to a Glutathione S-Transferase from Mango: Structure, Thermodynamics and Kinetics

Valenzuela-Chavira, I., Contreras-Vergara, C.A., Arvizu-Flores, A.A., Serrano-Posada, H., Lopez-Zavala, A.A., Garcia-Orozco, K.D., Hernandez-Paredes, J., Rudino-Pinera, E., Stojanoff, V., Sotelo-Mundo, R.R., Islas-Osuna, M.A.

(2017) Biochimie 135: 35

• PubMed: 28104507 
• DOI: https://doi.org/10.1016/j.biochi.2017.01.005
• Primary Citation Related Structures: 
  5G5E, 5G5F, 5KEJ


• PubMed Abstract: 
  

  We studied a mango glutathione S-transferase (GST) (Mangifera indica) bound to glutathione (GSH) and S-hexyl glutathione (GSX). This GST Tau class (MiGSTU) had a molecular mass of 25.5 kDa. MiGSTU Michaelis-Menten kinetic constants were determined for their substrates obtaining a K _m , V _max and k _cat for CDNB of 0.792 mM, 80.58 mM min ^-1 and 68.49 s ^-1 respectively and 0.693 mM, 105.32 mM min ^-1 and 89.57 s ^-1 , for reduced GSH respectively. MiGSTU had a micromolar affinity towards GSH (5.2 μM) or GSX (7.8 μM). The crystal structure of the MiGSTU in apo or bound to GSH or GSX generated a model that explains the thermodynamic signatures of binding and showed the importance of enthalpic-entropic compensation in ligand binding to Tau-class GST enzymes.

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Organizational Affiliation: 
• Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Hermosillo, Sonora 83304, Mexico; Laboratorio de Genética Molecular de Plantas, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Hermosillo, Sonora 83304, Mexico.
Laboratorio de Genética Molecular de Plantas, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Hermosillo, Sonora 83304, Mexico. Electronic address: [e-mail].
Departamento de Ciencias Químico Biológicas, Universidad de Sonora, Hermosillo, Sonora 83000, Mexico.
CONACyT, Laboratorio de Bioingeniería, Universidad de Colima, Coquimatlán, Colima 28629, Mexico.
Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Hermosillo, Sonora 83304, Mexico.
Departamento de Física, Universidad de Sonora, Hermosillo, Sonora 83000, Mexico.
Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos 62210, Mexico.
Brookhaven National Laboratory, Photon Science Directorate, Upton, NY 11973, USA.
Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Hermosillo, Sonora 83304, Mexico. Electronic address: [e-mail].
Laboratorio de Genética Molecular de Plantas, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Hermosillo, Sonora 83304, Mexico.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 26.28 kDa 
• Atom Count: 1,826 
• Modeled Residue Count: 219 
• Deposited Residue Count: 229 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TAU CLASS GLUTATHIONE S-TRANSFERASE	A	229	Mangifera indica	Mutation(s): 0  EC: 2.5.1.18
UniProt
Find proteins for A0A1P8NWC2 (Mangifera indica) Explore A0A1P8NWC2  Go to UniProtKB:  A0A1P8NWC2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSH	B [auth A]	Glutathione C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N
PEG	C [auth A], D [auth A], E [auth A], F [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002593 (GSH)	B [auth A]	Glutathione	Peptide-like / Oxidation-reduction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.243 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.483	α = 90
b = 48.24	β = 104.16
c = 52.684	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PROTEUM2	data reduction
SADABS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-01 
Deposition Author(s): Valenzuela-Chavira, I., Serrano-Posada, H., Lopez-Zavala, A., Hernandez-Paredes, J., Sotelo-Mundo, R.

Revision History  

• Version 1.0: 2017-02-01
  Type: Initial release
  
• Version 1.1: 2018-04-04
  Changes: Data collection
• Version 1.2: 2018-06-06
  Changes: Data collection, Refinement description
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description