1BHJ

CRYSTAL STRUCTURE OF APO-GLYCINE N-METHYLTRANSFERASE (GNMT)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of apo-glycine N-methyltransferase (GNMT).

Pattanayek, R.Newcomer, M.E.Wagner, C.

(1998) Protein Sci. 7: 1326-1331

  • DOI: 10.1002/pro.5560070608

  • PubMed Abstract: 
  • The crystal structure of the recombinant apo-form of glycine N-methyltransferase (GNMT) has been determined at 2.5 A resolution. GNMT is a tetrameric enzyme (monomer Mr = 32,423Da, 292 amino acids) that catalyzes the transfer of a methyl group from S ...

    The crystal structure of the recombinant apo-form of glycine N-methyltransferase (GNMT) has been determined at 2.5 A resolution. GNMT is a tetrameric enzyme (monomer Mr = 32,423Da, 292 amino acids) that catalyzes the transfer of a methyl group from S-adenosylmethionine (AdoMet) to glycine with the formation of S-adenosylhomocysteine (AdoHcy) and sarcosine (N-methylglycine). GNMT is a regulatory enzyme, which is inhibited by 5-methyltetrahydrofolate pentaglutamate and believed to control the ratio of AdoMet to AdoHcy in tissues. The crystals belong to the orthorhombic space group P2(1)2(1)2 (a = 85.39, b = 174.21, c = 44.71 A) and contain one dimer per asymmetric unit. The AdoMet-GNMT structure served as the starting model. The structure was refined to an R-factor of 21.9%. Each monomer is a three-domain structure with a large cavity enclosed by the three domains. The tetramer resembles a square with a central channel about which N-terminal domains are intertwined. Only localized changes of the residues involved in the binding pocket are observed for the apo-GNMT structure when compared to that determined in the presence of substrate and substrate analog.


    Organizational Affiliation

    Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA. pattanr@ctrvax.Vanderbilt.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLYCINE N-METHYLTRANSFERASE
A, B
292Rattus norvegicusGene Names: Gnmt
EC: 2.1.1.20
Find proteins for P13255 (Rattus norvegicus)
Go to UniProtKB:  P13255
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.221 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 85.390α = 90.00
b = 174.210β = 90.00
c = 44.710γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
DENZOdata reduction
X-PLORrefinement
X-PLORmodel building
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-01-06
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance