5HHY

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)

5HHY の概要

• エントリーDOI: 10.2210/pdb5hhy/pdb
• 関連するPDBエントリー: 5F9S
• 分子名称: Serine--pyruvate aminotransferase, (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE (3 entities in total)
• 機能のキーワード: aminotransferase, detoxification, liver, transferase
• 由来する生物種: Homo sapiens (Human)
• 細胞内の位置: Peroxisome : P21549
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 85252.33

構造登録者

Giardina, G.,Cutruzzola, F.,Borri Voltattorni, C.,Cellini, B.,Montioli, R. (登録日: 2016-01-11, 公開日: 2017-01-25, 最終更新日: 2024-01-10)

主引用文献

Giardina, G.,Paiardini, A.,Montioli, R.,Cellini, B.,Voltattorni, C.B.,Cutruzzola, F.
Radiation damage at the active site of human alanine:glyoxylate aminotransferase reveals that the cofactor position is finely tuned during catalysis.
Sci Rep, 7:11704-11704, 2017

PubMed Abstract: The alanine:glyoxylate aminotransferase (AGT), a hepatocyte-specific pyridoxal-5'-phosphate (PLP) dependent enzyme, transaminates L-alanine and glyoxylate to glycine and pyruvate, thus detoxifying glyoxylate and preventing pathological oxalate precipitation in tissues. In the widely accepted catalytic mechanism of the aminotransferase family, the lysine binding to PLP acts as a catalyst in the stepwise 1,3-proton transfer, interconverting the external aldimine to ketimine. This step requires protonation by a conserved aspartate of the pyridine nitrogen of PLP to enhance its ability to stabilize the carbanionic intermediate. The aspartate residue is also responsible for a significant geometrical distortion of the internal aldimine, crucial for catalysis. We present the structure of human AGT in which complete X-ray photoreduction of the Schiff base has occurred. This result, together with two crystal structures of the conserved aspartate pathogenic variant (D183N) and the molecular modeling of the transaldimination step, led us to propose that an interplay of opposite forces, which we named spring mechanism, finely tunes PLP geometry during catalysis and is essential to move the external aldimine in the correct position in order for the 1,3-proton transfer to occur.

PubMed: 28916765
DOI: 10.1038/s41598-017-11948-w

実験手法

X-RAY DIFFRACTION (1.7 Å)