Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 66.00 kDa 
• Atom Count: 4342 
• Modelled Residue Count: 554 
• Deposited Residue Count: 588 
• Unique protein chains: 1

1R74

Crystal Structure of Human Glycine N-Methyltransferase

• PDB DOI: 10.2210/pdb1R74/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-10-17 Released: 2004-09-21 
• Deposition Author(s): Pakhomova, S., Luka, Z., Wagner, C., Newcomer, M.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.266 
• R-Value Work: 0.222 
• R-Value Observed: 0.225 

Literature

Glycine N-methyltransferases: a comparison of the crystal structures and kinetic properties of recombinant human, mouse and rat enzymes.

Pakhomova, S., Luka, Z., Grohmann, S., Wagner, C., Newcomer, M.E.

(2004) Proteins 57: 331-337

• PubMed: 15340920 
• DOI: 10.1002/prot.20209
• Primary Citation of Related Structures:  
  1R74, 1R8X, 1R8Y


• PubMed Abstract: 
  

Glycine N-methyltransferases (GNMTs) from three mammalian sources were compared with respect to their crystal structures and kinetic parameters. The crystal structure for the rat enzyme was published previously. Human and mouse GNMT were expressed in Escherichia coli in order to determine their crystal structures. Mouse GNMT was crystallized in two crystal forms, a monoclinic form and a tetragonal form. Comparison of the three structures reveals subtle differences, which may relate to the different kinetic properties of the enzymes. The flexible character of several loops surrounding the active site, along with an analysis of the active site boundaries, indicates that the observed conformations of human and mouse GNMTs are more open than that of the rat enzyme. There is an increase in kcat when going from rat to mouse to human, suggesting a correlation with the increased flexibility of some structural elements of the respective enzymes.

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Organizational Affiliation: 

Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine N-methyltransferase	A, B	294	Homo sapiens	Mutation(s): 0  Gene Names: GNMT EC: 2.1.1.20
UniProt & NIH Common Fund Data Resources
Find proteins for Q14749 (Homo sapiens) Explore Q14749  Go to UniProtKB:  Q14749
PHAROS:  Q14749

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	D [auth A], H [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
BME	C [auth A], E [auth B], F [auth B], G [auth B]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.266 
• R-Value Work: 0.222 
• R-Value Observed: 0.225 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.84	α = 90
b = 83.23	β = 90
c = 114.88	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-10-17 
• Released Date: 2004-09-21 
Deposition Author(s): Pakhomova, S., Luka, Z., Wagner, C., Newcomer, M.E.

Revision History  

• Version 1.0: 2004-09-21
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description