8BIX

Cystathionine gamma-lyase N360S mutant from Toxoplasma gondii in complex with cystathionine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural basis of the inhibition of cystathionine gamma-lyase from Toxoplasma gondii by propargylglycine and cysteine.

Fernandez-Rodriguez, C.Conter, C.Oyenarte, I.Favretto, F.Quintana, I.Martinez-Chantar, M.L.Astegno, A.Martinez-Cruz, L.A.

(2023) Protein Sci 32: e4619-e4619

  • DOI: https://doi.org/10.1002/pro.4619
  • Primary Citation of Related Structures:  
    7NL1, 8BIS, 8BIU, 8BIV, 8BIW, 8BIX, 8BIZ

  • PubMed Abstract: 

    Cystathionine γ-lyase (CGL) is a PLP-dependent enzyme that catalyzes the last step of the reverse transsulfuration route for endogenous cysteine biosynthesis. The canonical CGL-catalyzed process consists of an α,γ-elimination reaction that breaks down cystathionine into cysteine, α-ketobutyrate, and ammonia. In some species, the enzyme can alternatively use cysteine as a substrate, resulting in the production of hydrogen sulfide (H 2 S). Importantly, inhibition of the enzyme and consequently of its H 2 S production activity, makes multiresistant bacteria considerably more susceptible to antibiotics. Other organisms, such as Toxoplasma gondii, the causative agent of toxoplasmosis, encode a CGL enzyme (TgCGL) that almost exclusively catalyzes the canonical process, with only minor reactivity to cysteine. Interestingly, the substitution of N360 by a serine (the equivalent amino acid residue in the human enzyme) at the active site changes the specificity of TgCGL for the catalysis of cystathionine, resulting in an enzyme that can cleave both the CγS and the CβS bond of cystathionine. Based on these findings and to deepen the molecular basis underlying the enzyme-substrate specificity, we have elucidated the crystal structures of native TgCGL and the variant TgCGL-N360S from crystals grown in the presence of cystathionine, cysteine, and the inhibitor d,l-propargylglycine (PPG). Our structures reveal the binding mode of each molecule within the catalytic cavity and help explain the inhibitory behavior of cysteine and PPG. A specific inhibitory mechanism of TgCGL by PPG is proposed.


  • Organizational Affiliation

    Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cystathionine beta-lyase, putativeA [auth C],
B [auth A]
417Toxoplasma gondiiMutation(s): 1 
Gene Names: BN1205_096960TGVEG_312930
EC: 4.4.1.1
UniProt
Find proteins for B6K8Y1 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore B6K8Y1 
Go to UniProtKB:  B6K8Y1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6K8Y1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.427α = 90
b = 158.427β = 90
c = 93.828γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
PHENIXrefinement
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministerio de Ciencia e Innovacion (MCIN)SpainBFU2010-17857
Ministerio de Ciencia e Innovacion (MCIN)SpainPID2019-109055RB-I00
Ministero dell Universita e della RicercaItaly2017ZBBYNC

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-12
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-03-06
    Changes: Structure summary