5DX5 | pdb_00005dx5

Crystal structure of methionine gamma-lyase from Clostridium sporogenes

• PDB DOI: https://doi.org/10.2210/pdb5DX5/pdb

• Classification: LYASE
• Organism(s): Clostridium sporogenes
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-09-23 Released: 2016-01-13 
• Deposition Author(s): Revtovich, S.V., Nikulin, A.D., Morozova, E.A., Anufrieva, N.V., Demidkina, T.V.
• Funding Organization(s): Russian Scientific Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 
  0.225 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Structure of methionine gamma-lyase from Clostridium sporogenes.

Revtovich, S., Anufrieva, N., Morozova, E., Kulikova, V., Nikulin, A., Demidkina, T.

(2016) Acta Crystallogr F Struct Biol Commun 72: 65-71

• PubMed: 26750487 
• DOI: https://doi.org/10.1107/S2053230X15023869
• Primary Citation Related Structures: 
  5DX5


• PubMed Abstract: 
  

  Methionine γ-lyase (MGL) is a pyridoxal 5'-phosphate-dependent enzyme that catalyzes the γ-elimination reaction of L-methionine. The enzyme is a promising target for therapeutic intervention in some anaerobic pathogens and has attracted interest as a potential cancer treatment. The crystal structure of MGL from Clostridium sporogenes has been determined at 2.37 Å resolution. The fold of the protein is similar to those of homologous enzymes from Citrobacter freundii, Entamoeba histolytica, Pseudomonas putida and Trichomonas vaginalis. A comparison of these structures revealed differences in the conformation of two flexible regions of the N- and C-terminal domains involved in the active-site architecture.

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Organizational Affiliation: 
• Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow 119991, Russian Federation.

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: 87.75 kDa 
• Atom Count: 6,319 
• Modeled Residue Count: 797 
• Deposited Residue Count: 800 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine gamma-lyase	A, B	400	Clostridium sporogenes	Mutation(s): 0  Gene Names: megL, CLOSPO_00030 EC: 4.4.1.11

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	C [auth A], E [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
CL	D [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free:  0.225 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.09	α = 90
b = 91.09	β = 90
c = 175.929	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
XDS	data reduction
SCALA	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-01-13 
Deposition Author(s): Revtovich, S.V., Nikulin, A.D., Morozova, E.A., Anufrieva, N.V., Demidkina, T.V.

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Funding Organization	Location	Grant Number
Russian Scientific Foundation	Russian Federation	15-14-00009

Revision History  

• Version 1.0: 2016-01-13
  Type: Initial release
  
• Version 1.1: 2016-01-20
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description