5HIJ

Crystal structure of glycine sarcosine N-methyltransferase from Methanohalophilus portucalensis in complex with betaine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Analysis of Glycine Sarcosine N-methyltransferase from Methanohalophilus portucalensis Reveals Mechanistic Insights into the Regulation of Methyltransferase Activity

Lee, Y.R.Lin, T.S.Lai, S.J.Liu, M.S.Lai, M.C.Chan, N.L.

(2016) Sci Rep 6: 38071-38071

  • DOI: 10.1038/srep38071
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Methyltransferases play crucial roles in many cellular processes, and various regulatory mechanisms have evolved to control their activities. For methyltransferases involved in biosynthetic pathways, regulation via feedback inhibition is a commonly e ...

    Methyltransferases play crucial roles in many cellular processes, and various regulatory mechanisms have evolved to control their activities. For methyltransferases involved in biosynthetic pathways, regulation via feedback inhibition is a commonly employed strategy to prevent excessive accumulation of the pathways' end products. To date, no biosynthetic methyltransferases have been characterized by X-ray crystallography in complex with their corresponding end product. Here, we report the crystal structures of the glycine sarcosine N-methyltransferase from the halophilic archaeon Methanohalophilus portucalensis (MpGSMT), which represents the first structural elucidation of the GSMT methyltransferase family. As the first enzyme in the biosynthetic pathway of the osmoprotectant betaine, MpGSMT catalyzes N-methylation of glycine and sarcosine, and its activity is feedback-inhibited by the end product betaine. A structural analysis revealed that, despite the simultaneous presence of both substrate (sarcosine) and cofactor (S-adenosyl-L-homocysteine; SAH), the enzyme was likely crystallized in an inactive conformation, as additional structural changes are required to complete the active site assembly. Consistent with this interpretation, the bound SAH can be replaced by the methyl donor S-adenosyl-L-methionine without triggering the methylation reaction. Furthermore, the observed conformational state was found to harbor a betaine-binding site, suggesting that betaine may inhibit MpGSMT activity by trapping the enzyme in an inactive form. This work implicates a structural basis by which feedback inhibition of biosynthetic methyltransferases may be achieved.


    Organizational Affiliation

    Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan.,Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan.,Institute of Biochemistry, National Chung Hsing University, Taichung 402, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycine sarcosine N-methyltransferase
A
284Methanohalophilus portucalensis FDF-1Mutation(s): 0 
Gene Names: gsmt
Find proteins for F6KV61 (Methanohalophilus portucalensis FDF-1)
Go to UniProtKB:  F6KV61
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BET
Query on BET

Download SDF File 
Download CCD File 
A
TRIMETHYL GLYCINE
C5 H12 N O2
KWIUHFFTVRNATP-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.166 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 52.176α = 90.00
b = 120.545β = 90.00
c = 131.368γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data processing
Blu-Icedata collection
PHENIXrefinement
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and TechnologyTaiwanNSC101-2911-I-002-303, 103-2113-M-002-010-MY3, 104-2911-I-002-302
National Taiwan UniversityTaiwan104R7614-3 and 104R7560-4
Ministry of Education, Taiwan ROC, under the ATU plan to NLCTaiwanNational Chung Hsing University

Revision History 

  • Version 1.0: 2016-11-23
    Type: Initial release
  • Version 1.1: 2017-01-18
    Type: Database references