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 
  • R-Value Observed: 0.178 

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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:  
    4L7Q, 4L8Y, 4L95, 4L8W, 4L8F

  • 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 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) ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Gamma-glutamyl hydrolaseD [auth A], C [auth B], A [auth C], B [auth D]312Danio rerioMutation(s): 1 
Gene Names: ggh
EC: 3.4.19.9
Find proteins for Q6NY42 (Danio rerio)
Explore Q6NY42 
Go to UniProtKB:  Q6NY42
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MTX
Query on MTX
Download Ideal Coordinates CCD File 
 E [auth D], F [auth B]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 
  • R-Value Observed: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.396α = 90
b = 198.098β = 113.816
c = 65.112γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
X-PLORmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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