5B5T | pdb_00005b5t

Crystal Structure of Escherichia coli Gamma-Glutamyltranspeptidase in Complex with peptidyl phosphonate inhibitor 1b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.194 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

Phosphonate-based irreversible inhibitors of human gamma-glutamyl transpeptidase (GGT). GGsTop is a non-toxic and highly selective inhibitor with critical electrostatic interaction with an active-site residue Lys562 for enhanced inhibitory activity

Kamiyama, A.Nakajima, M.Han, L.Wada, K.Mizutani, M.Tabuchi, Y.Kojima-Yuasa, A.Matsui-Yuasa, I.Suzuki, H.Fukuyama, K.Watanabe, B.Hiratake, J.

(2016) Bioorg Med Chem 24: 5340-5352

  • DOI: https://doi.org/10.1016/j.bmc.2016.08.050
  • Primary Citation of Related Structures:  
    5B5T

  • PubMed Abstract: 

    γ-Glutamyl transpeptidase (GGT, EC 2.3.2.2) that catalyzes the hydrolysis and transpeptidation of glutathione and its S-conjugates is involved in a number of physiological and pathological processes through glutathione metabolism and is an attractive pharmaceutical target. We report here the evaluation of a phosphonate-based irreversible inhibitor, 2-amino-4-{[3-(carboxymethyl)phenoxy](methoyl)phosphoryl}butanoic acid (GGsTop) and its analogues as a mechanism-based inhibitor of human GGT. GGsTop is a stable compound, but inactivated the human enzyme significantly faster than the other phosphonates, and importantly did not inhibit a glutamine amidotransferase. The structure-activity relationships, X-ray crystallography with Escherichia coli GGT, sequence alignment and site-directed mutagenesis of human GGT revealed a critical electrostatic interaction between the terminal carboxylate of GGsTop and the active-site residue Lys562 of human GGT for potent inhibition. GGsTop showed no cytotoxicity toward human fibroblasts and hepatic stellate cells up to 1mM. GGsTop serves as a non-toxic, selective and highly potent irreversible GGT inhibitor that could be used for various in vivo as well as in vitro biochemical studies.


  • Organizational Affiliation

    Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-glutamyltranspeptidase large chain
A, C
366Escherichia coli K-12Mutation(s): 0 
Gene Names: ggtb3447JW3412
EC: 2.3.2.2 (PDB Primary Data), 3.4.19.13 (PDB Primary Data)
UniProt
Find proteins for P18956 (Escherichia coli (strain K12))
Explore P18956 
Go to UniProtKB:  P18956
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18956
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-glutamyltranspeptidase small chain
B, D
190Escherichia coli K-12Mutation(s): 0 
Gene Names: ggtb3447JW3412
EC: 2.3.2.2 (PDB Primary Data), 3.4.19.13 (PDB Primary Data)
UniProt
Find proteins for P18956 (Escherichia coli (strain K12))
Explore P18956 
Go to UniProtKB:  P18956
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18956
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.194 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.99α = 90
b = 126.388β = 90
c = 129.075γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 6FYClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
MEXTJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2016-10-26
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2021-08-11
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.4: 2023-11-08
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-11-20
    Changes: Structure summary