Crystal structure of cystathionine gamma-lyase from Lactobacillus plantarum complexed with cystathionine

Experimental Data Snapshot

  • Resolution: 3.10 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.247 

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Catalytic specificity of the Lactobacillus plantarum cystathionine gamma-lyase presumed by the crystallographic analysis.

Matoba, Y.Noda, M.Yoshida, T.Oda, K.Ezumi, Y.Yasutake, C.Izuhara-Kihara, H.Danshiitsoodol, N.Kumagai, T.Sugiyama, M.

(2020) Sci Rep 10: 14886-14886

  • DOI: https://doi.org/10.1038/s41598-020-71756-7
  • Primary Citation of Related Structures:  
    6LDO, 6LE4

  • PubMed Abstract: 

    The reverse transsulfuration pathway, which is composed of cystathionine β-synthase (CBS) and cystathionine γ-lyase (CGL), plays a role to synthesize L-cysteine using L-serine and the sulfur atom in L-methionine. A plant-derived lactic acid bacterium Lactobacillus plantarum SN35N has been previously found to harbor the gene cluster encoding the CBS- and CGL-like enzymes. In addition, it has been demonstrated that the L. plantarum CBS can synthesize cystathionine from O-acetyl-L-serine and L-homocysteine. The aim of this study is to characterize the enzymatic functions of the L. plantarum CGL. We have found that the enzyme has the high γ-lyase activity toward cystathionine to generate L-cysteine, together with the β-lyase activity toward L-cystine to generate L-cysteine persulfide. By the crystallographic analysis of the inactive CGL K194A mutant complexed with cystathionine, we have found the residues which recognize the distal amino and carboxyl groups of cystathionine or L-cystine. The PLP-bound substrates at the active site may take either the binding pose for the γ- or β-elimination reaction, with the former being the major reaction in the case of cystathionine.

  • Organizational Affiliation

    Faculty of Pharmacy, Yasuda Women's University, Yasuhigashi 6-13-1, Asaminami-ku, Hiroshima, 731-0153, Japan. matoba@yasuda-u.ac.jp.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cystathionine gamma-lyase
A, B, C, D, E
A, B, C, D, E, F
389Lactiplantibacillus plantarumMutation(s): 1 
Gene Names: BIZ32_00995Nizo2891_3187
Find proteins for F9UT53 (Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1))
Explore F9UT53 
Go to UniProtKB:  F9UT53
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF9UT53
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
E9U (Subject of Investigation/LOI)
Query on E9U

Download Ideal Coordinates CCD File 
G [auth A]
H [auth B]
K [auth C]
M [auth D]
N [auth E]
G [auth A],
H [auth B],
K [auth C],
M [auth D],
N [auth E],
O [auth F]
(2~{S})-4-[(2~{R})-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]sulfanyl-2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]butanoic acid
C15 H22 N3 O9 P S
Query on PO4

Download Ideal Coordinates CCD File 
I [auth B],
J [auth B],
L [auth C]
O4 P
Experimental Data & Validation

Experimental Data

  • Resolution: 3.10 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.247 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 216.568α = 90
b = 200.738β = 117.21
c = 114.883γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-07
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description