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: 66.33 kDa 
• Atom Count: 4355 
• Modelled Residue Count: 553 
• Deposited Residue Count: 590 
• Unique protein chains: 1

2AZT

Crystal structure of H176N mutant of human Glycine N-Methyltransferase

• PDB DOI: 10.2210/pdb2AZT/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-09-12 Released: 2006-09-26 
• Deposition Author(s): Luka, Z., Pakhomova, S., Luka, Y., Newcomer, M.E., Wagner, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.282 
• R-Value Work: 0.236 
• R-Value Observed: 0.239 

Literature

Destabilization of human glycine N-methyltransferase by H176N mutation.

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

(2007) Protein Sci 16: 1957-1964

• PubMed: 17660255 
• DOI: 10.1110/ps.072921507
• Primary Citation of Related Structures:  
  2AZT


• PubMed Abstract: 
  

In the presence of moderate (2-4 M) urea concentrations the tetrameric enzyme, glycine N-methyltransferase (GNMT), dissociates into compact monomers. Higher concentrations of urea (7-8 M) promote complete denaturation of the enzyme. We report here that the H176N mutation in this enzyme, found in humans with hypermethioninaemia, significantly decreases stability of the tetramer, although H176 is located far from the intersubunit contact areas. Dissociation of the tetramer to compact monomers and unfolding of compact monomers of the mutant protein were detected by circular dichroism, quenching of fluorescence emission, size-exclusion chromatography, and enzyme activity. The values of apparent free energy of dissociation of tetramer and of unfolding of compact monomers for the H176N mutant (27.7 and 4.2 kcal/mol, respectively) are lower than those of wild-type protein (37.5 and 6.2 kcal/mol). A 2.7 A resolution structure of the mutant protein revealed no significant difference in the conformation of the protein near the mutated residue.

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Organizational Affiliation: 

Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine N-methyltransferase	A, B	295	Homo sapiens	Mutation(s): 1  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	E [auth A], J [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
BME	C [auth A], D [auth A], G [auth B], H [auth B], I [auth B]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
CL	F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.282 
• R-Value Work: 0.236 
• R-Value Observed: 0.239 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.116	α = 90
b = 83.279	β = 90
c = 115.45	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-09-12 
• Released Date: 2006-09-26 
Deposition Author(s): Luka, Z., Pakhomova, S., Luka, Y., Newcomer, M.E., Wagner, C.

Revision History  

• Version 1.0: 2006-09-26
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations