Structure of glycine N-methyltransferase complexed with S-adenosylmethionine and acetate, GNMT:SAM:Ace

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

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This is version 1.4 of the entry. See complete history


Catalytic mechanism of glycine N-methyltransferase

Takata, Y.Huang, Y.Komoto, J.Yamada, T.Konishi, K.Ogawa, H.Gomi, T.Fujioka, M.Takusagawa, F.

(2003) Biochemistry 42: 8394-8402

  • DOI: https://doi.org/10.1021/bi034245a
  • Primary Citation of Related Structures:  
    1NBH, 1NBI

  • PubMed Abstract: 

    Methyltransfer reactions are some of the most important reactions in biological systems. Glycine N-methyltransferase (GNMT) catalyzes the S-adenosyl-l-methionine- (SAM-) dependent methylation of glycine to form sarcosine. Unlike most SAM-dependent methyltransferases, GNMT has a relatively high value and is weakly inhibited by the product S-adenosyl-l-homocysteine (SAH). The major role of GNMT is believed to be the regulation of the cellular SAM/SAH ratio, which is thought to play a key role in SAM-dependent methyltransfer reactions. Crystal structures of GNMT complexed with SAM and acetate (a potent competitive inhibitor of Gly) and the R175K mutated enzyme complexed with SAM were determined at 2.8 and 3.0 A resolutions, respectively. With these crystal structures and the previously determined structures of substrate-free enzyme, a catalytic mechanism has been proposed. Structural changes occur in the transitions from the substrate-free to the binary complex and from the binary to the ternary complex. In the ternary complex stage, an alpha-helix in the N-terminus undergoes a major conformational change. As a result, the bound SAM is firmly connected to protein and a "Gly pocket" is created near the bound SAM. The second substrate Gly binds to Arg175 and is brought into the Gly pocket. Five hydrogen bonds connect the Gly in the proximity of the bound SAM and orient the lone pair orbital on the amino nitrogen (N) of Gly toward the donor methyl group (C(E)) of SAM. Thermal motion of the enzyme leads to a collision of the N and C(E) so that a S(N)2 methyltransfer reaction occurs. The proposed mechanism is supported by mutagenesis studies.

  • Organizational Affiliation

    Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas 66045-7534, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycine N-methyltransferase
A, B, C, D
292Rattus norvegicusMutation(s): 0 
Gene Names: GNMT
Find proteins for P13255 (Rattus norvegicus)
Explore P13255 
Go to UniProtKB:  P13255
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13255
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.05α = 90
b = 117.01β = 90
c = 137.78γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-03-04
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Advisory, Refinement description
  • Version 1.4: 2024-02-14
    Changes: Advisory, Data collection, Database references, Derived calculations