5X1L

Vanillate/3-O-methylgallate O-demethylase, LigM, tetrahydrofolate complex form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of a new O-demethylase from Sphingobium sp. strain SYK-6

Harada, A.Kamimura, N.Takeuchi, K.Yu, H.Y.Masai, E.Senda, T.

(2017) FEBS J. 284: 1855-1867

  • DOI: 10.1111/febs.14085
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In the cell, tetrahydrofolate (H4 folate) derivatives with a C1 unit are utilized in various ways, such as for the synthesis of amino acids and nucleic acids. While H4 folate derivatives with the C1 unit are typically produced in the glycine cleavage ...

    In the cell, tetrahydrofolate (H4 folate) derivatives with a C1 unit are utilized in various ways, such as for the synthesis of amino acids and nucleic acids. While H4 folate derivatives with the C1 unit are typically produced in the glycine cleavage system, Sphingobium sp. strain SYK-6, which can utilize lignin-derived aromatic compounds as a sole source of carbon and energy, lacks this pathway, probably due to its unique nutrient requirements. In this bacterium, H4 folate-dependent O-demethylases in catabolic pathways for lignin-derived aromatic compounds seem to be involved in the C1 metabolism. LigM is one of the O-demethylases and catalyzes a C1-unit transfer from vanillate (VNL) to H4 folate. As the primary structure of LigM shows a similarity to T-protein in the glycine cleavage system, we hypothesized that LigM has evolved from T-protein, acquiring its unique biochemical and biological functions. To prove this hypothesis, structure-based understanding of its catalytic reaction is essential. Here, we determined the crystal structure of LigM in apo form and in complex with substrates and H4 folate. These crystal structures showed that the overall structure of LigM is similar to T-protein, but LigM has a few distinct characteristics, particularly in the active site. Structure-based mutational analysis revealed that His60 and Tyr247, which are not conserved in T-protein, are essential to the catalytic activity of LigM and their interactions with the oxygen atom in the methoxy group of VNL seem to facilitate a methyl moiety (C1-unit) transfer to H4 folate. Taken together, our structural data suggest that LigM has evolved divergently from T-protein.


    Organizational Affiliation

    Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vanillate/3-O-methylgallate O-demethylase
A, B, C
474Sphingobium sp. (strain NBRC 103272 / SYK-6)Mutation(s): 0 
Gene Names: ligM
Find proteins for G2IQS7 (Sphingobium sp. (strain NBRC 103272 / SYK-6))
Go to UniProtKB:  G2IQS7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
THG
Query on THG

Download SDF File 
Download CCD File 
B, C
(6S)-5,6,7,8-TETRAHYDROFOLATE
C19 H23 N7 O6
MSTNYGQPCMXVAQ-RYUDHWBXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 102.773α = 90.00
b = 117.888β = 90.00
c = 129.726γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-01-26 
  • Released Date: 2017-05-17 
  • Deposition Author(s): Harada, A., Senda, T.

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan14J04356
the Ministry of Education, Culture, Sports, Science and TechnologyJapanPlatform for Drug Discovery, Informatics, and Structural Life Science
Japan Agency for Medical Research and Development (AMED)JapanPlatform for Drug Discovery, Informatics, and Structural Life Science

Revision History 

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2017-05-31
    Type: Database references
  • Version 1.2: 2017-06-28
    Type: Database references