7F1V

Crystal structure of Pseudomonas putida methionine gamma-lyase Q349S mutant with L-homocysteine intermediates


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Characterization and application of l-methionine gamma-lyase Q349S mutant enzyme with an enhanced activity toward l-homocysteine.

Okawa, A.Handa, H.Yasuda, E.Murota, M.Kudo, D.Tamura, T.Shiba, T.Inagaki, K.

(2022) J Biosci Bioeng 133: 213-221

  • DOI: https://doi.org/10.1016/j.jbiosc.2021.11.008
  • Primary Citation of Related Structures:  
    7F1P, 7F1U, 7F1V

  • PubMed Abstract: 

    l-Methionine γ-lyse (MGL), a pyridoxal 5'-phosphate-dependent enzyme, catalyzes the α,γ-elimination of l-methionine (l-Met) and l-homocysteine (l-Hcy) to produce α-keto acids, thiols, and ammonia. Previously, various mutant enzymes of Pseudomonas putida MGL (PpMGL) were prepared to identify a homocysteine (Hcy)-specific enzyme that would assist the diagnosis of homocystinuria. Among the mutat enzymes the Q349S mutant exhibited high degradation activity toward l-Hcy. In the present study, PpMGL Q349S was characterized; the results suggested that it could be applied to determine the amount of l-Hcy. Compared to the wild-type PpMGL, specific activities of the Q349S mutant with l-Hcy and l-Met were 1.5 and 0.7 times, respectively. Additionally, we confirmed that l-Hcy in plasma samples could be accurately detected using the Q349S mutant by preincubating it with cysteine desulfurase (CsdA). Furthermore, we determined the X-ray crystal structure of PpMGL Q349S l-Met or l-Hcy complexes Michaelis complex, germinal diamine, and external aldimine at 2.25-2.40 Å. These 3D structures showed that the interaction partner of the β-hydroxyl group of Thr355 in the wild-type PpMGL was changed to the carboxyl group of the Hcy-PLP external aldimine in the Q349S mutant. The interaction of Ser349 and Arg375 was different between l-Met and l-Hcy recognition, indicating that it was important for the recognition of the carboxyl group of the substrate.


  • Organizational Affiliation

    Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan. Electronic address: pn2b9nr4@s.okayama-u.ac.jp.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-methionine gamma-lyase
A, C
398Pseudomonas putidaMutation(s): 1 
Gene Names: mdeA
EC: 4.4.1.11 (PDB Primary Data), 4.4.1.2 (PDB Primary Data)
UniProt
Find proteins for P13254 (Pseudomonas putida)
Explore P13254 
Go to UniProtKB:  P13254
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13254
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
L-methionine gamma-lyase
B, D
398Pseudomonas putidaMutation(s): 1 
Gene Names: mdeA
EC: 4.4.1.11 (PDB Primary Data), 4.4.1.2 (PDB Primary Data)
UniProt
Find proteins for P13254 (Pseudomonas putida)
Explore P13254 
Go to UniProtKB:  P13254
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13254
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7XF (Subject of Investigation/LOI)
Query on 7XF

Download Ideal Coordinates CCD File 
E [auth A],
F [auth C]
(2~{S})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-4-sulfanyl-butanoic acid
C12 H19 N2 O7 P S
PXCMMZUTCUCUSM-JTQLQIEISA-N
HCS (Subject of Investigation/LOI)
Query on HCS

Download Ideal Coordinates CCD File 
G [auth D]2-AMINO-4-MERCAPTO-BUTYRIC ACID
C4 H9 N O2 S
FFFHZYDWPBMWHY-VKHMYHEASA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LLP
Query on LLP
B, D
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.075α = 90
b = 152.299β = 90
c = 80.508γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-20
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-03-13
    Changes: Structure summary