PDBsum entry: 2nmp

Lyase

PDB id: 2nmp

Contents

Protein chains

376 a.a. *

Ligands

PLP ×3

Waters ×157

* Residue conservation analysis

PDB id:

2nmp

Name:

Lyase

Title:

Crystal structure of human cystathionine gamma lyase

Structure:

Cystathionine gamma-lyase. Chain: a, b, c, d. Fragment: residues 1-402. Synonym: gamma-cystathionase. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: cth. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.60Å R-factor: 0.180 R-free: 0.245

Authors:

T.Karlberg,J.Uppenberg,C.Arrowsmith,H.Berglund,R.D.Busam,R.C A.Edwards,U.B.Ericsson,S.Flodin,A.Flores,S.Graslund,B.M.Hal M.Hammarstrom,M.Hogbom,I.Johansson,T.Kotenyova,A.Magnusdott M.Moche,M.E.Nilsson,P.Nordlund,T.Nyman,D.Ogg,C.Persson,J.Sa P.Stenmark,M.Sundstrom,A.G.Thorsell,S.Van-Den-Berg,K.Wallde J.Weigelt,L.Holmberg-Schiavone,Structural Genomics Consorti

Key ref:

Q.Sun et al. (2009). Structural basis for the inhibition mechanism of human cystathionine gamma-lyase, an enzyme responsible for the production of H(2)S. J Biol Chem, 284, 3076-3085. PubMed id: 19019829 DOI: 10.1074/jbc.M805459200

Date:

23-Oct-06 Release date: 07-Nov-06

Protein chains

P32929  (CGL_HUMAN) -  Cystathionine gamma-lyase

Seq: 405 a.a.

Struc: 376 a.a.

Enzyme reactions

• Enzyme class: E.C.4.4.1.1 - Cystathionine gamma-lyase.
• Reaction: L-cystathionine + H₂O = L-cysteine + NH₃ + 2-oxobutanoate
• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PLP) matches with 93.75% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (2 terms)
• Biological process: metabolic process (12 terms)
• Biochemical function: catalytic activity (6 terms)

reference

DOI no: 10.1074/jbc.M805459200

J Biol Chem 284:3076-3085 (2009)

PubMed id: 19019829

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

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

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.

Selected figure(s)

Figure 1.
Crystal structure of hCSE. a, ribbon diagram of the hCSE monomer. N and C termini are labeled. The large PLP binding domain is shown in red, the small domain in green, and PLP in yellow. Panels b and c are the superimposed apo-hCSE (blue) and PLP complex (red) active site regions. The Met^110–Asn^118 region (b) and loop Thr^211–Met^214 (c) are shown. The root mean square deviation between two superimposed models is 1.5 Å for 336 Cα atoms. PLP, Tyr^114, and Lys^212 are shown in stick representations. d, stereoview of the 2F[o] - F[c] simulated annealing omit map of PLP from hCSE·PLP. All atoms within 3.5 Å of PLP were omitted prior to refinement. The map was contoured at a level of 1.0σ. These figures were prepared using the program PyMol (32). Shown is the electrostatic surface potential at the active site region of apo-hCSE (e) and hCSE·PLP (f). Apo-hCSE shows significant enlarged (open) surface. These figures were prepared using the program GRASP (33).

Figure 5.
Mechanism of PAG inhibition on hCSE. Upon the addition of the inhibitor, the α-amino group of PAG is first deprotonated by Arg^62 of the adjacent monomer (B:) (Step 1) for transaldimination to occur (Step 2). Lys^212 then abstracts a proton from the β-position of the bound alkyne to generate an activated allene (Step 3), which is then attacked by the hydroxyl group of Tyr^114 (Step 4) to produce a vinyl ether. Subsequent transaldimination with Lys^212 (Step 5) regenerates the internal aldimine.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 3076-3085) copyright 2009.

Figures were selected by an automated process.