Structural mechanism of enzyme mistargeting in hereditary kidney stone disease in vitro

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.223 

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Structural implications of a G170R mutation of alanine:glyoxylate aminotransferase that is associated with peroxisome-to-mitochondrion mistargeting.

Djordjevic, S.Zhang, X.Bartlam, M.Ye, S.Rao, Z.Danpure, C.J.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 233-236

  • DOI: https://doi.org/10.1107/S1744309109054645
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    In a subset of patients with the hereditary kidney-stone disease primary hyperoxaluria type 1 (PH1), the liver-specific enzyme alanine:glyoxylate aminotransferase (AGT) is mistargeted from peroxisomes to mitochondria. This is a consequence of the combined presence of the common P11L polymorphism and a disease-specific G170R mutation. In this paper, the crystal structure of mutant human AGT containing the G170R replacement determined at a resolution of 2.6 A is reported. The crystal structure of AGT consists of an intimate dimer in which an extended N-terminal segment of 21 amino acids from one subunit wraps as an elongated irregular coil around the outside of the crystallographic symmetry-related subunit. In addition to the N-terminal segment, the monomer structure contains a large domain of 261 amino acids and a small C-terminal domain of 110 amino acids. Comparison of the mutant AGT structure and that of wild-type normal AGT shows that the two structures are almost identical, with a backbone-atom r.m.s. deviation of 0.34 A. However, evidence of significant local structural changes in the vicinity of the G170R mutation might be linked to the apparent decrease in protein stability.

  • Organizational Affiliation

    Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, England.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
alanine--glyoxylate aminotransferase392Homo sapiensMutation(s): 1 
EC: (PDB Primary Data), (PDB Primary Data)
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
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.223 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.491α = 90
b = 89.491β = 90
c = 142.823γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-11-11
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2018-07-25
    Changes: Data collection, Database references, Refinement description, Source and taxonomy, Structure summary
  • Version 1.4: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.6: 2023-11-15
    Changes: Data collection