1H0C

The crystal structure of human alanine:glyoxylate aminotransferase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.231 

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


Literature

Crystal Structure of Alanine:Glyoxylate Aminotransferase and the Relationship between Genotype and Enzymatic Phenotype in Primary Hyperoxaluria Type 1.

Zhang, X., Roe, S.M., Roe, S.M., Hou, Y., Bartlam, M., Rao, Z., Pearl, L.H., Danpure, C.J.

(2003) J Mol Biol 331: 643

  • DOI: 10.1016/s0022-2836(03)00791-5
  • Primary Citation of Related Structures:  
    1H0C

  • PubMed Abstract: 

    • A deficiency of the liver-specific enzyme alanine:glyoxylate aminotransferase (AGT) is responsible for the potentially lethal hereditary kidney stone disease primary hyperoxaluria type 1 (PH1). Many of the mutations in the gene encoding AGT are associate ...

    A deficiency of the liver-specific enzyme alanine:glyoxylate aminotransferase (AGT) is responsible for the potentially lethal hereditary kidney stone disease primary hyperoxaluria type 1 (PH1). Many of the mutations in the gene encoding AGT are associated with specific enzymatic phenotypes such as accelerated proteolysis (Ser205Pro), intra-peroxisomal aggregation (Gly41Arg), inhibition of pyridoxal phosphate binding and loss of catalytic activity (Gly82Glu), and peroxisome-to-mitochondrion mistargeting (Gly170Arg). Several mutations, including that responsible for AGT mistargeting, co-segregate and interact synergistically with a Pro11Leu polymorphism found at high frequency in the normal population. In order to gain further insights into the mechanistic link between genotype and enzymatic phenotype in PH1, we have determined the crystal structure of normal human AGT complexed to the competitive inhibitor amino-oxyacetic acid to 2.5A. Analysis of this structure allows the effects of these mutations and polymorphism to be rationalised in terms of AGT tertiary and quaternary conformation, and in particular it provides a possible explanation for the Pro11Leu-Gly170Arg synergism that leads to AGT mistargeting.

    Organizational Affiliation: 

    Department of Biology, University College London, Gower Street, London WC1E 6BT, UK.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SERINE--GLYOXYLATE AMINOTRANSFERASE A392Homo sapiensMutation(s): 0 
Gene Names: AGXT, AGT1, SPAT
EC: 2.6.1.44 (PDB Primary Data), 2.6.1.51 (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: 2.50 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.231 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.33α = 90
b = 90.33β = 90
c = 142.01γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
SOLVE/RESOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-12
    Type: Initial release
  • Version 1.1: 2011-10-12
    Changes: Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation, Other