3ELP

Structure of cystationine gamma lyase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for the inhibition mechanism of human cystathionine gamma-lyase, an enzyme responsible for the production of H(2)S

Sun, Q.Collins, R.Huang, S.Holmberg-Schiavone, L.Anand, G.S.Tan, C.H.van-den-Berg, S.Deng, L.-W.Moore, P.K.Karlberg, T.Sivaraman, J.

(2009) J Biol Chem 284: 3076-3085

  • DOI: 10.1074/jbc.M805459200
  • Primary Citation of Related Structures:  
    3COG, 3ELP, 2NMP

  • PubMed Abstract: 
  • Impairment of the formation or action of hydrogen sulfide (H(2)S), an endogenous gasotransmitter, is associated with various diseases, such as hypertension, diabetes mellitus, septic and hemorrhagic shock, and pancreatitis. Cystathionine beta-synthase and cystathionine gamma-lyase (CSE) are two pyridoxal-5'-phosphate (PLP)-dependent enzymes largely responsible for the production of H(2)S in mammals ...

    Impairment of the formation or action of hydrogen sulfide (H(2)S), an endogenous gasotransmitter, is associated with various diseases, such as hypertension, diabetes mellitus, septic and hemorrhagic shock, and pancreatitis. Cystathionine beta-synthase and cystathionine gamma-lyase (CSE) are two pyridoxal-5'-phosphate (PLP)-dependent enzymes largely responsible for the production of H(2)S in mammals. Inhibition of CSE by DL-propargylglycine (PAG) has been shown to alleviate disease symptoms. Here we report crystal structures of human CSE (hCSE), in apo form, and in complex with PLP and PLP.PAG. Structural characterization, combined with biophysical and biochemical studies, provides new insights into the inhibition mechanism of hCSE-mediated production of H(2)S. Transition from the open form of apo-hCSE to the closed PLP-bound form reveals large conformational changes hitherto not reported. In addition, PAG binds hCSE via a unique binding mode, not observed in PAG-enzyme complexes previously. The interaction of PAG-hCSE was not predicted based on existing information from known PAG complexes. The structure of hCSE.PLP.PAG complex highlights the particular importance of Tyr(114) in hCSE and the mechanism of PAG-dependent inhibition of hCSE. These results provide significant insights, which will facilitate the structure-based design of novel inhibitors of hCSE to aid in the development of therapies for diseases involving disorders of sulfur metabolism.


    Organizational Affiliation

    Department of Biological Sciences, National University of Singapore, Singapore.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cystathionine gamma-lyaseB [auth A], A [auth B], C, D410Homo sapiensMutation(s): 0 
Gene Names: CTH
EC: 4.4.1.1
Find proteins for P32929 (Homo sapiens)
Explore P32929 
Go to UniProtKB:  P32929
NIH Common Fund Data Resources
PHAROS:  P32929
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.222 
  • Space Group: P 42
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.304α = 90
b = 121.304β = 90
c = 125.592γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2008-09-23 
  • Released Date: 2008-11-18 
  • Deposition Author(s): Sun, Q., Sivaraman, J.

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description