Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33.54 kDa 
• Atom Count: 2130 
• Residue Count: 249 
• Unique protein chains: 1

5GWX

Crystal structure of glycine sarcosine N-methyltransferase from Methanohalophilus portucalensis in complex with S-adenosylmethionine and sarcosine

• DOI: 10.2210/pdb5GWX/pdb

• Classification: TRANSFERASE
• Organism(s): Methanohalophilus portucalensis FDF-1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-09-14 Released: 2016-11-23 
• Deposition Author(s): Lee, Y.R., Lin, T.S., Lai, S.J., Liu, M.S., Lai, M.C., Chan, N.L.
• Funding Organization(s): Ministry of Science and Technology, National Taiwan University, Ministry of Education, Taiwan ROC, under the ATU plan to NLC

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.204 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 

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

• PubMed: 27934872 
• DOI: 10.1038/srep38071
• Primary Citation of Related Structures:  
  5GWX, 5HII, 5HIK, 5HIJ, 5HIM, 5HIL, 5H02


• 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 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.

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Organizational Affiliation: 

Institute of Biochemistry, National Chung Hsing University, Taichung 402, Taiwan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine sarcosine N-methyltransferase	A	284	Methanohalophilus portucalensis FDF-1	Mutation(s): 0  Gene Names: gsmt, EFE41_00900, MPF_0823, SAMN06264941_0527
Find proteins for F6KV61 (Methanohalophilus portucalensis FDF-1) Explore F6KV61  Go to UniProtKB:  F6KV61

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	A	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
SAR	A	SARCOSINE C3 H7 N O2 FSYKKLYZXJSNPZ-UHFFFAOYSA-N
EDO	A	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.204 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.733	α = 90
b = 120.71	β = 90
c = 130.922	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Blu-Ice	data collection
HKL-2000	data scaling
HKL-2000	data processing
PHENIX	model building
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-09-14 
• Released Date: 2016-11-23 
Deposition Author(s): Lee, Y.R., Lin, T.S., Lai, S.J., Liu, M.S., Lai, M.C., Chan, N.L.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology	Taiwan	NSC101-2911-I-002-303, 103-2113-M-002-010-MY3, 104-2911-I-002-302
National Taiwan University	Taiwan	104R7614-3 and 104R7560-4
Ministry of Education, Taiwan ROC, under the ATU plan to NLC	Taiwan	National Chung Hsing University

Revision History 

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