3JWA

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1134/S0006297911050063
  • Primary Citation of Related Structures:  

  • 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 det ...

    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.


    Organizational Affiliation

    Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow. tvd@eimb.ru




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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPJ
Query on MPJ

Download SDF File 
Download CCD File 
A
(1-AMINO-3-METHYLSULFANYL-PROPYL)-PHOSPHINIC ACID
METHIONINE PHOSPHINATE
C4 H12 N O2 P S
CZRBNMUARBZMHQ-SCSAIBSYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
LLP
Query on LLP
A
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.141 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 56.420α = 90.00
b = 123.010β = 90.00
c = 127.010γ = 90.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
XSCALEdata scaling
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-11-05
    Type: Database references