1J04

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.223 

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This is version 1.3 of the entry. See complete history. 


Literature

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: 10.1107/S1744309109054645
  • Primary Citation of Related Structures:  
    1J04

  • 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 combine ...

    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.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
alanine--glyoxylate aminotransferase A392Homo sapiensMutation(s): 1 
Gene Names: AGXT, AGT1, SPAT
EC: 2.6.1.51 (PDB Primary Data), 2.6.1.44 (PDB Primary Data)
Find proteins for P21549 (Homo sapiens)
Explore P21549 
Go to UniProtKB:  P21549
NIH Common Fund Data Resources
PHAROS:  P21549
GTEx:  ENSG00000172482
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • 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