3COG | pdb_00003cog

Crystal structure of human cystathionase (Cystathionine gamma lyase) in complex with DL-propargylglycine

• PDB DOI: https://doi.org/10.2210/pdb3COG/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-03-28 Released: 2008-05-27 
• Deposition Author(s): Collins, R., Karlberg, T., Lehtio, L., Arrowsmith, C.H., Berglund, H., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, I., Kallas, A., Kotenyova, T., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Olesen, K., Persson, C., Schuler, H., Svensson, L., Thorsell, A.G., Tresaugues, L., Van den Berg, S., Sagermark, J., Busam, R.D., Welin, M., Weigelt, J., Wikstrom, M., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.204 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

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 Biological Chem 284: 3076-3085

• PubMed: 19019829 
• DOI: https://doi.org/10.1074/jbc.M805459200
• Primary Citation Related Structures: 
  2NMP, 3COG, 3ELP


• 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. 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.

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Organizational Affiliation: 
• Department of Biological Sciences, National University of Singapore, 117543 Singapore.
Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm SE-17177, Sweden.
Department of Chemistry, National University of Singapore, 117543 Singapore.
Department of Biochemistry, National University of Singapore, 117543 Singapore.
Pharmaceutical Sciences Division, King's College, University of London, London, United Kingdom.
Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm SE-17177, Sweden. Electronic address: [e-mail].
Department of Biological Sciences, National University of Singapore, 117543 Singapore. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 179.18 kDa 
• Atom Count: 13,153 
• Modeled Residue Count: 1,531 
• Deposited Residue Count: 1,612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystathionine gamma-lyase	A, B, C, D	403	Homo sapiens	Mutation(s): 0  Gene Names: CTH EC: 4.4.1.1 (PDB Primary Data), 4.4.1.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P32929 (Homo sapiens) Explore P32929  Go to UniProtKB:  P32929
PHAROS:  P32929 GTEx:  ENSG00000116761

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	F [auth A], K [auth C], O [auth D]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
2AG	G [auth A], L [auth C], P [auth D]	(2S)-2-aminopent-4-enoic acid C5 H9 N O2 WNNNWFKQCKFSDK-BYPYZUCNSA-N
PEG	I [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	H [auth A], M [auth C], Q [auth D], R [auth D], S [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NO3	E [auth A], J [auth C], N [auth D]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.204 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.35	α = 90
b = 107.22	β = 90
c = 153.31	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-27 
Deposition Author(s): Collins, R., Karlberg, T., Lehtio, L., Arrowsmith, C.H., Berglund, H., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, I., Kallas, A., Kotenyova, T., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Olesen, K., Persson, C., Schuler, H., Svensson, L., Thorsell, A.G., Tresaugues, L., Van den Berg, S., Sagermark, J., Busam, R.D., Welin, M., Weigelt, J., Wikstrom, M., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-05-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description