5X2W

Crystal structure of Pseudomonas putida methionine gamma-lyase wild type with L-methionine intermediates


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and mechanistic insights into homocysteine degradation by a mutant of methionine gamma-lyase based on substrate-assisted catalysis

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

(2017) Protein Sci. 26: 1224-1230

  • DOI: 10.1002/pro.3158
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Methionine γ-lyse (MGL) catalyzes the α, γ-elimination of l-methionine and its derivatives as well as the α, β-elimination of l-cysteine and its derivatives to produce α-keto acids, volatile thiols, and ammonia. The reaction mechanism of MGL has been ...

    Methionine γ-lyse (MGL) catalyzes the α, γ-elimination of l-methionine and its derivatives as well as the α, β-elimination of l-cysteine and its derivatives to produce α-keto acids, volatile thiols, and ammonia. The reaction mechanism of MGL has been characterized by enzymological studies using several site-directed mutants. The Pseudomonas putida MGL C116H mutant showed drastically reduced degradation activity toward methionine while retaining activity toward homocysteine. To understand the underlying mechanism and to discern the subtle differences between these substrates, we analyzed the crystal structures of the reaction intermediates. The complex formed between the C116H mutant and methionine demonstrated that a loop structure (Ala51-Asn64) in the adjacent subunit of the catalytic dimer cannot approach the cofactor pyridoxal 5'-phosphate (PLP) because His116 disrupts the interaction of Asp241 with Lys240, and the liberated side chain of Lys240 causes steric hindrance with this loop. Conversely, in the complex formed between C116H mutant and homocysteine, the thiol moiety of the substrate conjugated with PLP offsets the imidazole ring of His116 via a water molecule, disrupting the interaction of His116 and Asp241 and restoring the interaction of Asp241 with Lys240. These structural data suggest that the Cys116 to His mutation renders the enzyme inactive toward the original substrate, but activity is restored when the substrate is homocysteine due to substrate-assisted catalysis.


    Organizational Affiliation

    Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Kyoto, 606-8585, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-methionine gamma-lyase
A, B, C, D
398Pseudomonas putidaMutation(s): 0 
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
3LM
Query on 3LM

Download SDF File 
Download CCD File 
A, B, C, D
(2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-4-(methylsulfanyl)but-2-enoic acid
C13 H19 N2 O7 P S
LPFNPHQQDYAHKU-QDEBKDIKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 154.635α = 90.00
b = 152.311β = 90.00
c = 80.487γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-04-12
    Type: Initial release
  • Version 1.1: 2017-06-07
    Type: Database references