4OMA

The crystal structure of methionine gamma-lyase from Citrobacter freundii in complex with L-cycloserine pyridoxal-5'-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.139 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Pre-steady-state Kinetic and Structural Analysis of Interaction of Methionine gamma-Lyase from Citrobacter freundii with Inhibitors.

Kuznetsov, N.A.Faleev, N.G.Kuznetsova, A.A.Morozova, E.A.Revtovich, S.V.Anufrieva, N.V.Nikulin, A.D.Fedorova, O.S.Demidkina, T.V.

(2015) J.Biol.Chem. 290: 671-681

  • DOI: 10.1074/jbc.M114.586511

  • PubMed Abstract: 
  • Methionine γ-lyase (MGL) catalyzes the γ-elimination of l-methionine and its derivatives as well as the β-elimination of l-cysteine and its analogs. These reactions yield α-keto acids and thiols. The mechanism of chemical conversion of amino acids in ...

    Methionine γ-lyase (MGL) catalyzes the γ-elimination of l-methionine and its derivatives as well as the β-elimination of l-cysteine and its analogs. These reactions yield α-keto acids and thiols. The mechanism of chemical conversion of amino acids includes numerous reaction intermediates. The detailed analysis of MGL interaction with glycine, l-alanine, l-norvaline, and l-cycloserine was performed by pre-steady-state stopped-flow kinetics. The structure of side chains of the amino acids is important both for their binding with enzyme and for the stability of the external aldimine and ketimine intermediates. X-ray structure of the MGL·l-cycloserine complex has been solved at 1.6 Å resolution. The structure models the ketimine intermediate of physiological reaction. The results elucidate the mechanisms of the intermediate interconversion at the stages of external aldimine and ketimine formation.


    Organizational Affiliation

    From the Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, the Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090.




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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LCS
Query on LCS

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A
[5-hydroxy-6-methyl-4-({[(4E)-3-oxo-1,2-oxazolidin-4-ylidene]amino}methyl)pyridin-3-yl]methyl dihydrogen phosphate
C11 H14 N3 O7 P
KFCQHWOGBVCKHR-UKTHLTGXSA-N
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
PGE
Query on PGE

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A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.139 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 56.270α = 90.00
b = 122.890β = 90.00
c = 126.610γ = 90.00
Software Package:
Software NamePurpose
PHASESphasing
MAR345dtbdata collection
REFMACrefinement
PROCESSdata scaling
PROCESSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-26
    Type: Initial release
  • Version 1.1: 2014-12-03
    Type: Database references
  • Version 1.2: 2015-01-21
    Type: Database references