3VK4

Crystal Structure of L-Methionine gamma-Lyase from Pseudomonas putida C116H Mutant complexed with L-homocysteine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The Role of Amino Acid Residues in the Active Site of LPseudomonas putida.

Fukumoto, M.Kudou, D.Murano, S.Shiba, T.Sato, D.Tamura, T.Harada, S.Inagaki, K.

(2012) Biosci.Biotechnol.Biochem. 76: 1275-1284

  • DOI: 10.1271/bbb.110906
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cys116, Lys240*, and Asp241* (asterisks indicate residues from the second subunit of the active dimer) at the active site of L-methionine γ-lyase of Pseudomonas putida (MGL_Pp) are highly conserved among heterologous MGLs. In a previous study, we fou ...

    Cys116, Lys240*, and Asp241* (asterisks indicate residues from the second subunit of the active dimer) at the active site of L-methionine γ-lyase of Pseudomonas putida (MGL_Pp) are highly conserved among heterologous MGLs. In a previous study, we found that substitution of Cys116 for His led to a drastic increase in activity toward L-cysteine and a decrease in that toward L-methionine. In this study, we examined some properties of the C116H mutant by kinetic analysis and 3D structural analysis. We assumed that substitution of Cys116 for His broke the original hydrogen-bond network and that this induced a significant effect of Tyr114 as a general acid catalyst, possibly due to the narrow space in the active site. The C116H mutant acquired a novel β-elimination activity and lead a drastic conformation change in the histidine residue at position 116 by binding the substrate, suggesting that this His residue affects the reaction specificity of C116H. Furthermore, we suggest that Lys240* is important for substrate recognition and structural stability and that Asp241* is also involved in substrate specificity in the elimination reaction. Based on this, we suggest that the hydrogen-bond network among Cys116, Lys240*, and Asp241* contributes to substrate specificity that is, to L-methionine recognition at the active site in MGL_Pp.


    Organizational Affiliation

    Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan. kinagaki@cc.okayama-u.ac.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methionine gamma-lyase
A, B, C, D
398Pseudomonas putidaMutation(s): 1 
Gene Names: mdeA
EC: 4.4.1.11
Find proteins for P13254 (Pseudomonas putida)
Go to UniProtKB:  P13254
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HCS
Query on HCS

Download SDF File 
Download CCD File 
A, B, C, D
2-AMINO-4-MERCAPTO-BUTYRIC ACID
C4 H9 N O2 S
FFFHZYDWPBMWHY-VKHMYHEASA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A, B, C, D
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 153.488α = 90.00
b = 153.487β = 90.00
c = 80.671γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-19
    Type: Initial release