Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 86623.59 
• Atom Count: 6032 
• Residue Count: 776 
• Unique protein chains: 1

2YOB

High resolution AGXT_M structure

• DOI: 10.2210/pdb2YOB/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 5 


• Deposited: 2012-10-22 Released: 2013-10-30 
• Deposition Author(s): Fabelo-Rosa, I., Mesa-Torres, N., Riverol, D., Yunta, C., Albert, A., Salido, E., Pey, A.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.204 
• R-Value Work: 0.170 

Literature

The Role of Protein Denaturation Energetics and Molecular Chaperones in the Aggregation and Mistargeting of Mutants Causing Primary Hyperoxaluria Type I

Mesa-Torres, N., Fabelo-Rosa, I., Riverol, D., Yunta, C., Albert, A., Salido, E., Pey, A.L.

(2013) Plos One 8: 71963

• PubMed: 24205397 
• DOI: 10.1371/journal.pone.0071963


• PubMed Abstract: 
  

Primary hyperoxaluria type I (PH1) is a conformational disease which result in the loss of alanine:glyoxylate aminotransferase (AGT) function. The study of AGT has important implications for protein folding and trafficking because PH1 mutants may cause protein aggregation and mitochondrial mistargeting. We herein describe a multidisciplinary study aimed to understand the molecular basis of protein aggregation and mistargeting in PH1 by studying twelve AGT variants. Expression studies in cell cultures reveal strong protein folding defects in PH1 causing mutants leading to enhanced aggregation, and in two cases, mitochondrial mistargeting. Immunoprecipitation studies in a cell-free system reveal that most mutants enhance the interactions with Hsc70 chaperones along their folding process, while in vitro binding experiments show no changes in the interaction of folded AGT dimers with the peroxisomal receptor Pex5p. Thermal denaturation studies by calorimetry support that PH1 causing mutants often kinetically destabilize the folded apo-protein through significant changes in the denaturation free energy barrier, whereas coenzyme binding overcomes this destabilization. Modeling of the mutations on a 1.9 Å crystal structure suggests that PH1 causing mutants perturb locally the native structure. Our work support that a misbalance between denaturation energetics and interactions with chaperones underlie aggregation and mistargeting in PH1, suggesting that native state stabilizers and protein homeostasis modulators are potential drugs to restore the complex and delicate balance of AGT protein homeostasis in PH1.

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Organizational Affiliation: 

Department of Physical Chemistry, Faculty of Sciences, University of Granada, Granada, Spain.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
SERINE--PYRUVATE AMINOTRANSFERASE	A, B	388	Homo sapiens	Mutation(s): 5  Gene Names: AGXT (AGT1, SPAT) EC: 2.6.1.51
Find proteins for P21549 (Homo sapiens) Go to Gene View: AGXT Go to UniProtKB:  P21549

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	A, B	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BTB	A, B	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL BIS-TRIS BUFFER C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N
PLP	A, B	PYRIDOXAL-5'-PHOSPHATE VITAMIN B6 Phosphate C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.204 
• R-Value Work: 0.170 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 54.495	α = 90.00
b = 103.525	β = 90.00
c = 153.832	γ = 90.00

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-10-22 
• Released Date: 2013-10-30 
• Deposition Author(s): Fabelo-Rosa, I., Mesa-Torres, N., Riverol, D., Yunta, C., Albert, A., Salido, E., Pey, A.L.

Revision History 

• Version 1.0: 2013-10-30
  Type: Initial release
• Version 1.1: 2013-11-20
  Type: Database references