Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40.38 kDa 
• Atom Count: 3087 
• Modelled Residue Count: 361 
• Deposited Residue Count: 364 
• Unique protein chains: 1

1WOS

Crystal Structure of T-protein of the Glycine Cleavage System

• PDB DOI: 10.2210/pdb1WOS/pdb

• Classification: TRANSFERASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-08-24 Released: 2004-09-07 
• Deposition Author(s): Lee, H.H., Kim, D.J., Ahn, H.J., Ha, J.Y., Suh, S.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.248 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 

Literature

Crystal Structure of T-protein of the Glycine Cleavage System: Cofactor binding, insights into H-protein recognition, and molecular basis for understanding nonketotic hyperglycinemia

Lee, H.H., Kim, D.J., Ahn, H.J., Ha, J.Y., Suh, S.W.

(2004) J Biol Chem 279: 50514-50523

• PubMed: 15355973 
• DOI: 10.1074/jbc.M409672200
• Primary Citation of Related Structures:  
  1WOO, 1WOP, 1WOR, 1WOS


• PubMed Abstract: 
  

The glycine cleavage system catalyzes the oxidative decarboxylation of glycine in bacteria and in mitochondria of animals and plants. Its deficiency in human causes nonketotic hyperglycinemia, an inborn error of glycine metabolism. T-protein, one of the four components of the glycine cleavage system,is a tetrahydrofolate dependent aminomethyltransferase. It catalyzes the transfer of the methylene carbon unit to tetrahydrofolate from the methylamine group covalently attached to the lipoamide arm of H-protein. To gain insight into the T-protein function at the molecular level, we have determined the first crystal structure of T-protein from Thermotoga maritima by the multiwavelength anomalous diffraction method of x-ray crystallography and refined four structures: the apoform; the tetrahydrofolate complex; the folinic acid complex; and the lipoic acid complex. The overall fold of T-protein is similar to that of the C-terminal tetrahydrofolate-binding region (residues 421-830) of Arthrobacter globiformis dimethylglycine oxidase. Tetrahydrofolate (or folinic acid) is bound near the center of the tripartite T-protein. Lipoic acid is bound adjacent to the tetrahydrofolate binding pocket, thus defining the interaction surface for H-protein binding. A homology model of the human T-protein provides the structural framework for understanding the molecular mechanisms underlying the development of nonketotic hyperglycinemia due to missense mutations of the human T-protein.

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Organizational Affiliation: 

Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Korea.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminomethyltransferase	A	364	Thermotoga maritima	Mutation(s): 0  EC: 2.1.2.10
UniProt
Find proteins for Q9WY54 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WY54  Go to UniProtKB:  Q9WY54

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.248 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.365	α = 90
b = 53.852	β = 90
c = 149.157	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-08-24 
• Released Date: 2004-09-07 
Deposition Author(s): Lee, H.H., Kim, D.J., Ahn, H.J., Ha, J.Y., Suh, S.W.

Revision History  

• Version 1.0: 2004-09-07
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance