Cystathionine beta-synthase from Toxoplasma gondii

Experimental Data Snapshot

  • Resolution: 3.20 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.254 

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Structural insight into the unique conformation of cystathionine beta-synthase from Toxoplasma gondii .

Fernandez-Rodriguez, C.Oyenarte, I.Conter, C.Gonzalez-Recio, I.Nunez-Franco, R.Gil-Pitarch, C.Quintana, I.Jimenez-Oses, G.Dominici, P.Martinez-Chantar, M.L.Astegno, A.Martinez-Cruz, L.A.

(2021) Comput Struct Biotechnol J 19: 3542-3555

  • DOI: https://doi.org/10.1016/j.csbj.2021.05.052
  • Primary Citation of Related Structures:  
    6XWL, 6XYL, 6Z3S, 6ZS7

  • PubMed Abstract: 

    Cysteine plays a major role in the redox homeostasis and antioxidative defense mechanisms of many parasites of the phylum Apicomplexa. Of relevance to human health is Toxoplasma gondii , the causative agent of toxoplasmosis. A major route of cysteine biosynthesis in this parasite is the reverse transsulfuration pathway involving two key enzymes cystathionine β-synthase (CBS) and cystathionine γ-lyase (CGL). CBS from T. gondii ( Tg CBS) catalyzes the pyridoxal-5́-phosphate-dependent condensation of homocysteine with either serine or O -acetylserine to produce cystathionine. The enzyme can perform alternative reactions that use homocysteine and cysteine as substrates leading to the endogenous biosynthesis of hydrogen sulfide, another key element in maintaining the intracellular redox equilibrium. In contrast with human CBS, Tg CBS lacks the N-terminal heme binding domain and is not responsive to S-adenosylmethionine. Herein, we describe the structure of a Tg CBS construct that lacks amino acid residues 466-491 and shows the same activity of the native protein. Tg CBS Δ466-491 was determined alone and in complex with reaction intermediates. A complementary molecular dynamics analysis revealed a unique domain organization, similar to the pathogenic mutant D444N of human CBS. Our data provides one missing piece in the structural diversity of CBSs by revealing the so far unknown three-dimensional arrangement of the CBS-type of Apicomplexa. This domain distribution is also detected in yeast and bacteria like Pseudomonas aeruginosa . These results pave the way for understanding the mechanisms by which Tg CBS regulates the intracellular redox of the parasite, and have far-reaching consequences for the functional understanding of CBSs with similar domain distribution.

  • Organizational Affiliation

    Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cystathionine beta-synthase514Toxoplasma gondii ME49Mutation(s): 0 
Gene Names: TGME49_259180
Find proteins for A0A125YSJ9 (Toxoplasma gondii (strain ATCC 50611 / Me49))
Explore A0A125YSJ9 
Go to UniProtKB:  A0A125YSJ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A125YSJ9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.20 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.254 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.237α = 90
b = 83.237β = 90
c = 420.309γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
autoPROCdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Economy and Competitiveness (MINECO)SpainBFU2013-47531-R
Ministry of Economy and Competitiveness (MINECO)SpainBES-2014-068464
Ministry of Economy and Competitiveness (MINECO)SpainBFU2016-77408-R
Ministry of Economy and Competitiveness (MINECO)SpainBES-2017-080435

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-03
    Type: Initial release
  • Version 1.1: 2021-08-04
    Changes: Database references