4L8F

Crystal structure of gamma-glutamyl hydrolase (C108A) complex with MTX

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

Structural insights into the hydrolysis and polymorphism of methotrexate polyglutamate by zebrafish gamma-glutamyl hydrolase

Chuankhayan, P., Kao, T.-T., Lin, C.-C., Guan, H.-H., Nakagawa, A., Fu, T.-F., Chen, C.-J.

(2013) J.Med.Chem. 56: 7625-7635

  • DOI: 10.1021/jm401013e
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • γ-Glutamyl hydrolases (γGH) catalyze the hydrolysis of γ-linked glutamate residues from the polyglutamyl of folates and antifolates, such as methotrexate (MTX), a widely used anticancer drug. We describe the first crystal structures of the endopeptid ...

    γ-Glutamyl hydrolases (γGH) catalyze the hydrolysis of γ-linked glutamate residues from the polyglutamyl of folates and antifolates, such as methotrexate (MTX), a widely used anticancer drug. We describe the first crystal structures of the endopeptidase-type γGH (zγGH) from zebrafish and the mutant complexes with MTX(Glu)5 and hydrolyzed MTX(Glu)1, revealing the complete set of key residues involved in hydrolysis as well as the substrate-binding subsites (-1 to +2). The side chain of Phe20 and the 6-methylpterin ring of MTX(Glu)5 invoke π-π interactions to promote distinct concerted conformational alterations involving ∼90° rotations in the complexes with the zγGH-C108A and zγGH-H218N mutant proteins. The structural geometries of the MTX(Glu)5 and hydrolyzed MTX(Glu)1 in the mutant complexes differ significantly from those of the previously known MTX(Glu)1, providing polymorphic information. Together with the structural comparison and the activity analysis, these results shed light on the catalytic mechanism and substrate recognition of zγGH and other γ-glutamyl hydrolases.

    Organizational Affiliation: 

    Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center , Hsinchu 30076, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gamma-glutamyl hydrolase
C, D, B, A
312Danio rerioMutation(s): 1 
Gene Names: ggh
EC: 3.4.19.9
Find proteins for Q6NY42 (Danio rerio)
Go to UniProtKB:  Q6NY42
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MTX
Query on MTX
Download SDF File 
Download CCD File 
B, D
METHOTREXATE
C20 H22 N8 O5
FBOZXECLQNJBKD-ZDUSSCGKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.175 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 53.396α = 90.00
b = 198.098β = 113.82
c = 65.112γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
X-PLORmodel building
ADSCdata collection
REFMACrefinement
X-PLORphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-14
    Type: Initial release