3MKJ

Methionine gamma-lyase from Citrobacter freundii with pyridoximine-5'-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Exploring methionine gamma-lyase structure-function relationship via microspectrophotometry and X-ray crystallography

Ronda, L.Bazhulina, N.P.Morozova, E.A.Revtovich, S.V.Chekhov, V.O.Nikulin, A.D.Demidkina, T.V.Mozzarelli, A.

(2011) Biochim.Biophys.Acta 1814: 834-842

  • DOI: 10.1016/j.bbapap.2010.06.017

  • PubMed Abstract: 
  • Pyridoxal 5'-phosphate (PLP) dependent methionine γ-lyase catalyzes the breakdown of L-methionine to α-ketobutyric acid, methanethiol and ammonia. This enzyme, present in anaerobic microorganisms, has biomedical interest both for its activity as anti ...

    Pyridoxal 5'-phosphate (PLP) dependent methionine γ-lyase catalyzes the breakdown of L-methionine to α-ketobutyric acid, methanethiol and ammonia. This enzyme, present in anaerobic microorganisms, has biomedical interest both for its activity as antitumor agent, depleting methionine supply in methionine-dependent cancers, and as target in the treatment of human pathogen infections, activating the pro-drug trifluoromethionine. To validate the structure of the enzyme from Citrobacter freundii, crystallized from monomethyl ether polyethylene glycol 2000, for the development of lead compounds, the reactivity of the crystalline enzyme towards L-methionine, substrate analogs and inhibitors was determined by polarized absorption microspectrophotometry. Spectral data were also collected for enzyme crystals, grown in monomethyl ether polyethylene glycol 2000 in the presence of ammonium sulfate. The three-dimensional structure of these enzyme crystals, solved at 1.65Å resolution with R(free) 23.2%, revealed the surprising absence of the aldimine bond between the active site Lys210 and PLP. Different hypothesis are proposed and discussed in the light of spectral and structural data, pointing out to the relevance of the complementarity between X-ray crystallography and single crystal spectroscopy for the understanding of biological mechanisms at molecular level. This article is part of a Special Issue entitled: Protein Structure and Function in the Crystalline State.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Parma, Parma, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methionine gamma-lyase
A
398Citrobacter freundiiMutation(s): 0 
Gene Names: megL
Find proteins for Q84AR1 (Citrobacter freundii)
Go to UniProtKB:  Q84AR1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PZP
Query on PZP

Download SDF File 
Download CCD File 
A
[5-hydroxy-4-(iminomethyl)-6-methyl-pyridin-3-yl]methyl dihydrogen phosphate
pyridoximine-5'-phosphate
C8 H11 N2 O5 P
CLOXDHRIVOURLQ-XNWCZRBMSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.196 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 56.690α = 90.00
b = 122.800β = 90.00
c = 128.040γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
MAR345dtbdata collection
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-03-05
    Type: Database references