Crystal structure of Human Cystathionine gamma lyase with S-3-Carboxpropyl-L-Cysteine

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 

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S-3-Carboxypropyl-l-cysteine specifically inhibits cystathionine gamma-lyase-dependent hydrogen sulfide synthesis.

Yadav, P.K.Vitvitsky, V.Kim, H.White, A.Cho, U.S.Banerjee, R.

(2019) J Biol Chem 294: 11011-11022

  • DOI: https://doi.org/10.1074/jbc.RA119.009047
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Hydrogen sulfide (H 2 S) is a gaseous signaling molecule, which modulates a wide range of mammalian physiological processes. Cystathionine γ-lyase (CSE) catalyzes H 2 S synthesis and is a potential target for modulating H 2 S levels under pathophysiological conditions. CSE is inhibited by propargylglycine (PPG), a widely used mechanism-based inhibitor. In this study, we report that inhibition of H 2 S synthesis from cysteine, but not the canonical cystathionine cleavage reaction catalyzed by CSE in vitro , is sensitive to preincubation of the enzyme with PPG. In contrast, the efficacy of S -3-carboxpropyl-l-cysteine (CPC) a new inhibitor described herein, was not dependent on the order of substrate/inhibitor addition. We observed that CPC inhibited the γ-elimination reaction of cystathionine and H 2 S synthesis from cysteine by human CSE with K i values of 50 ± 3 and 180 ± 15 μm, respectively. We noted that CPC spared the other enzymes involved either directly (cystathionine β-synthase and mercaptopyruvate sulfurtransferase) or indirectly (cysteine aminotransferase) in H 2 S biogenesis. CPC also targeted CSE in cultured cells, inhibiting transsulfuration flux by 80-90%, as monitored by the transfer of radiolabel from [ 35 S]methionine to GSH. The 2.5 Å resolution crystal structure of human CSE in complex with the CPC-derived aminoacrylate intermediate provided a structural framework for the molecular basis of its inhibitory effect. In summary, our study reveals a previously unknown confounding effect of PPG, widely used to inhibit CSE-dependent H 2 S synthesis, and reports on an alternative inhibitor, CPC, which could be used as a scaffold to develop more potent H 2 S biogenesis inhibitors.

  • Organizational Affiliation

    Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109 and.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cystathionine gamma-lyase
A, B, C, D
402Homo sapiensMutation(s): 0 
Gene Names: CTH
UniProt & NIH Common Fund Data Resources
Find proteins for P32929 (Homo sapiens)
Explore P32929 
Go to UniProtKB:  P32929
PHAROS:  P32929
GTEx:  ENSG00000116761 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32929
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.551α = 90
b = 152.167β = 112.25
c = 83.771γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL58984

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-12
    Type: Initial release
  • Version 1.1: 2019-06-19
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-24
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description