Molecular defects of the glycine 41 variants of alanine glyoxylate aminotransferase associated with primary hyperoxaluria type I.


Abstract

G41 is an interfacial residue located within the alpha-helix 34-42 of alanine:glyoxylate aminotransferase (AGT). Its mutations on the major (AGT-Ma) or the minor (AGT-Mi) allele give rise to the variants G41R-Ma, G41R-Mi, and G41V-Ma causing hyperoxaluria type 1. Impairment of dimerization in these variants has been suggested to be responsible for immunoreactivity deficiency, intraperoxisomal aggregation, and sensitivity to proteasomal degradation. However, no experimental evidence supports this view. Here we report that G41 mutations, besides increasing the dimer-monomer equilibrium dissociation constant, affect the protein conformation and stability, and perturb its active site. As compared to AGT-Ma or AGT-Mi, G41 variants display different near-UV CD and intrinsic emission fluorescence spectra, larger exposure of hydrophobic surfaces, sensitivity to Met53-Tyr54 peptide bond cleavage by proteinase K, decreased thermostability, reduced coenzyme binding affinity, and catalytic efficiency. Additionally, unlike AGT-Ma and AGT-Mi, G41 variants under physiological conditions form insoluble inactive high-order aggregates (approximately 5,000 nm) through intermolecular electrostatic interactions. A comparative molecular dynamics study of the putative structures of AGT-Mi and G41R-Mi predicts that G41 --> R mutation causes a partial unwinding of the 34-42 alpha-helix and a displacement of the first 44 N-terminal residues including the active site loop 24-32. These simulations help us to envisage the possible structural basis of AGT dysfunction associated with G41 mutations. The detailed insight into how G41 mutations act on the structure-function of AGT may contribute to achieve the ultimate goal of correcting the effects of these mutations. Study holds ProTherm entries: 25440, 25441, 25442, 25443, 25444, 25445, 25446, 25447, 25448 Extra Details: mutations on the major (AGT-Ma) allele; holo form dimer interface; pathogenic variant; protein aggregation; pyridoxal 5'-phosphate

Submission Details

ID: 5HtmSPMV4

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:55 p.m.

Version: 1

Publication Details
Cellini B;Montioli R;Paiardini A;Lorenzetto A;Maset F;Bellini T;Oppici E;Voltattorni CB,Proc. Natl. Acad. Sci. U.S.A. (2010) Molecular defects of the glycine 41 variants of alanine glyoxylate aminotransferase associated with primary hyperoxaluria type I. PMID:20133649
Additional Information

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P
 

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)


Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
5HHY 2017-01-25 1.7 Structure of human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma) showing X-Ray induced reduction of PLP internal aldimine to 4'-deoxy-piridoxine-phosphate (PLR)
5F9S 2016-12-21 1.7 Crystal structure of human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma) at 1.7 Angstrom; internal aldimine with PLP in the active site
5LUC 2017-09-20 1.8 Crystal structure of the D183N variant of human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma) at 1.8 Angstrom; internal aldimine with PLP in the active site
2YOB 2013-10-30 1.9 High resolution AGXT_M structure
4KYO 2014-11-19 2.2 Alanine-glyoxylate aminotransferase variant K390A in complex with the TPR domain of human Pex5p
4CBR 2014-07-09 2.3 X-ray structure of the more stable human AGXT triple mutant (AGXT_HEM)
4CBS 2014-07-09 2.3 X-ray structure of quintuple mutant of human alanine glyoxylate aminotransferase, AGXT_RHEAM
3R9A 2011-05-11 2.35 Human alanine-glyoxylate aminotransferase in complex with the TPR domain of human PEX5P
5OG0 2017-09-27 2.5 Crystal structure of human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma) at 2.5 Angstrom; internal aldimine with PLP in the active site
1H0C 2003-06-12 2.5 The crystal structure of human alanine:glyoxylate aminotransferase
1J04 2003-11-11 2.6 Structural mechanism of enzyme mistargeting in hereditary kidney stone disease in vitro
5OFY 2017-09-27 2.8 Crystal structure of the D183N variant of human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma) at pH 9.0. 2.8 Ang; internal aldimine with PLP in the active site
4KXK 2014-11-19 2.9 Alanine-glyoxylate aminotransferase variant K390A/K391A in complex with the TPR domain of human Pex5p
4I8A 2013-05-01 2.9 Alanine-glyoxylate aminotransferase variant S187F

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
95.4 Serine--pyruvate aminotransferase Q5RDP0 SPYA_PONAB
100.0 Serine--pyruvate aminotransferase P21549 SPYA_HUMAN