3JWA

Crystal structure of L-methionine gamma-lyase from Citrobacter freundii with methionine phosphinate

• PDB DOI: https://doi.org/10.2210/pdb3JWA/pdb

• Classification: LYASE
• Organism(s): Citrobacter freundii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-09-18 Released: 2010-09-08 
• Deposition Author(s): Revtovish, S.V., Nikulin, A.D., Morozova, E.A., Demidkina, T.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.182 
• R-Value Work: 0.141 
• R-Value Observed: 0.143 

Literature

Three-dimensional structures of noncovalent complexes of Citrobacter freundii methionine gamma-lyase with substrates.

Revtovich, S.V., Morozova, E.A., Khurs, E.N., Zakomirdina, L.N., Nikulin, A.D., Demidkina, T.V., Khomutov, R.M.

(2011) Biochemistry (Mosc) 76: 564-570

• PubMed: 21639836 
• DOI: https://doi.org/10.1134/S0006297911050063
• Primary Citation of Related Structures:  
  3JW9, 3JWA, 3JWB


• PubMed Abstract: 
  

  Crystal structures of Citrobacter freundii methionine γ-lyase complexes with the substrates of γ- (L-1-amino-3-methylthiopropylphosphinic acid) and β- (S-ethyl-L-cysteine) elimination reactions and the competitive inhibitor L-norleucine have been determined at 1.45, 1.8, and 1.63 Å resolution, respectively. All three amino acids occupy the active site of the enzyme but do not form a covalent bond with pyridoxal 5'-phosphate. Hydrophobic interactions between the active site residues and the side groups of the substrates and the inhibitor are supposed to cause noncovalent binding. Arg374 and Ser339 are involved in the binding of carboxyl groups of the substrates and the inhibitor. The hydroxyl of Tyr113 is a potential acceptor of a proton from the amino groups of the amino acids.

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Organizational Affiliation: 

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow. [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: 43.88 kDa 
• Atom Count: 3,445 
• Modelled Residue Count: 396 
• Deposited Residue Count: 398 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine gamma-lyase	A	398	Citrobacter freundii	Mutation(s): 0  Gene Names: megL EC: 4.4.1.11
UniProt
Find proteins for Q84AR1 (Citrobacter freundii) Explore Q84AR1  Go to UniProtKB:  Q84AR1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPJ	B [auth A]	(1-AMINO-3-METHYLSULFANYL-PROPYL)-PHOSPHINIC ACID C4 H12 N O2 P S CZRBNMUARBZMHQ-SCSAIBSYSA-N
PEG	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS
LLP	A	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.182 
• R-Value Work: 0.141 
• R-Value Observed: 0.143 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.42	α = 90
b = 123.01	β = 90
c = 127.01	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHENIX	model building
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-08 
Deposition Author(s): Revtovish, S.V., Nikulin, A.D., Morozova, E.A., Demidkina, T.V.

Revision History  

• Version 1.0: 2010-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-11-05
  Changes: Database references
• Version 1.3: 2020-10-21
  Changes: Data collection, Derived calculations
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2023-11-22
  Changes: Data collection