3R9A

Human alanine-glyoxylate aminotransferase in complex with the TPR domain of human PEX5P

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Molecular requirements for peroxisomal targeting of alanine-glyoxylate aminotransferase as an essential determinant in primary hyperoxaluria type 1

Fodor, K., Wolf, J., Erdmann, R., Schliebs, W., Wilmanns, M.

(2012) PLoS Biol 10: e1001309-e1001309

  • DOI: 10.1371/journal.pbio.1001309
  • Primary Citation of Related Structures:  
    3R9A

  • PubMed Abstract: 

    • Alanine-glyoxylate aminotransferase is a peroxisomal enzyme, of which various missense mutations lead to irreversible kidney damage via primary hyperoxaluria type 1, in part caused by improper peroxisomal targeting. To unravel the molecular mechanism of ...

    Alanine-glyoxylate aminotransferase is a peroxisomal enzyme, of which various missense mutations lead to irreversible kidney damage via primary hyperoxaluria type 1, in part caused by improper peroxisomal targeting. To unravel the molecular mechanism of its recognition by the peroxisomal receptor Pex5p, we have determined the crystal structure of the respective cargo-receptor complex. It shows an extensive protein/protein interface, with contributions from residues of the peroxisomal targeting signal 1 and additional loops of the C-terminal domain of the cargo. Sequence segments that are crucial for receptor recognition and hydrophobic core interactions within alanine-glyoxylate aminotransferase are overlapping, explaining why receptor recognition highly depends on a properly folded protein. We subsequently characterized several enzyme variants in vitro and in vivo and show that even minor protein fold perturbations are sufficient to impair Pex5p receptor recognition. We discuss how the knowledge of the molecular parameters for alanine-glyoxylate aminotransferase required for peroxisomal translocation could become useful for improved hyperoxaluria type 1 treatment.

    Organizational Affiliation: 

    European Molecular Biology Laboratory Hamburg, Hamburg, Germany.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine--pyruvate aminotransferase A, C394Homo sapiensMutation(s): 0 
Gene Names: AGT1, AGXT, 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
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Peroxisomal targeting signal 1 receptor B, D328Homo sapiensMutation(s): 0 
Gene Names: PEX5, PXR1
Find proteins for P50542 (Homo sapiens)
Explore P50542 
Go to UniProtKB:  P50542
NIH Common Fund Data Resources
PHAROS:  P50542
GTEx:  ENSG00000139197
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BTB
Query on BTB
Download Ideal Coordinates CCD File 
C
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP		A,CL-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.367α = 90
b = 99.156β = 96.66
c = 127.698γ = 90
Software Package:
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2011-03-25 
  • Released Date: 2011-05-11 
    • Deposition Author(s): Fodor, K., Wilmanns, M.
  • This entry supersedes: 3IMZ

Revision History 

  • Version 1.0: 2011-05-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-05-02
    Changes: Database references