Crystal Structure of cystathionine gamma-lyase from yeast

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.346 
  • R-Value Work: 0.253 

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Determinants of Enzymatic Specificity in the Cys-Met-Metabolism PLP-Dependent Enzymes Family: Crystal Structure of Cystathionine gamma-lyase from Yeast and Intrafamiliar Structural Comparison

Messerschmidt, A.Worbs, M.Steegborn, C.Wahl, M.C.Huber, R.Laber, B.Clausen, T.

(2003) Biol Chem 384: 373-386

  • DOI: https://doi.org/10.1515/BC.2003.043
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The crystal structure of cystathionine gamma-lyase (CGL) from yeast has been solved by molecular replacement at a resolution of 2.6 A. The molecule consists of 393 amino acid residues and one PLP moiety and is arranged in the crystal as a tetramer with D2 symmetry as in other related enzymes of the Cys-Met-metabolism PLP-dependent family like cystathionine beta-lyase (CBL). A structure comparison with other family members revealed surprising insights into the tuning of enzymatic specificity between the different family members. CGLs from yeast or human are virtually identical at their active sites to cystathionine gamma-synthase (CGS) from E. coli. Both CGLs and bacterial CGSs exhibit gamma-synthase and gamma-lyase activities depending on their position in the metabolic pathway and the available substrates. This group of enzymes has a glutamate (E333 in yeast CGL) which binds to the distal group of cystathionine (CTT) or the amino group of cysteine. Plant CGSs use homoserine phosphate instead of O-succinyl-homoserine as one substrate. This is reflected by a partially different active site structure in plant CGSs. In CGL and CBL the pseudosymmetric substrate must dock at the active site in different orientations, with S in gamma-position (CBL) or in delta-position (CGL). The conserved glutamate steers the substrate as seen in other CGLs. In CBLs this position is occupied by either tyrosine or hydrophobic residues directing binding of CTT such that S is in the in gamma-position. In methionine gamma-lyase a hydrophic patch operates as recognition site for the methyl group of the methionine substrate.

  • Organizational Affiliation

    Max-Planck-Institut for Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18a, D-82152 Planegg-Martinsried, Germany.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cystathionine gamma-lyase
A, B, C, D
393Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CYS3
Find proteins for P31373 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P31373 
Go to UniProtKB:  P31373
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31373
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.346 
  • R-Value Work: 0.253 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.819α = 90
b = 62.164β = 105.42
c = 160.837γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-12-04
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description