High resolution AGXT_M structure

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


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

  • DOI: https://doi.org/10.1371/journal.pone.0071963
  • Primary Citation of Related Structures:  

  • 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
388Homo sapiensMutation(s): 5 
UniProt & NIH Common Fund Data Resources
Find proteins for P21549 (Homo sapiens)
Explore P21549 
Go to UniProtKB:  P21549
PHAROS:  P21549
GTEx:  ENSG00000172482 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21549
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PLP

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
C8 H10 N O6 P
Query on BTB

Download Ideal Coordinates CCD File 
D [auth A],
L [auth B]
C8 H19 N O5
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
M [auth B]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
M [auth B],
N [auth B]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.495α = 90
b = 103.525β = 90
c = 153.832γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-30
    Type: Initial release
  • Version 1.1: 2013-11-20
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description