4AB7

Crystal structure of a tetrameric acetylglutamate kinase from Saccharomyces cerevisiae complexed with its substrate N- acetylglutamate

4AB7 の概要

• エントリーDOI: 10.2210/pdb4ab7/pdb
• 関連するPDBエントリー: 3ZZF 3ZZG 3ZZH 3ZZI
• 分子名称: PROTEIN ARG5,6, MITOCHONDRIAL, N-ACETYL-L-GLUTAMATE (2 entities in total)
• 機能のキーワード: transferase, arginine biosynthesis, amino acid kinase domain, gcn5-related acetyltransferase, gnat, duf619
• 由来する生物種: SACCHAROMYCES CEREVISIAE (BAKER'S YEAST)
• タンパク質・核酸の鎖数: 8
• 化学式量合計: 411099.08

構造登録者

de Cima, S.,Gil-Ortiz, F.,Crabeel, M.,Fita, I.,Rubio, V. (登録日: 2011-12-07, 公開日: 2012-05-02, 最終更新日: 2023-12-20)

主引用文献

De Cima, S.,Gil-Ortiz, F.,Crabeel, M.,Fita, I.,Rubio, V.
Insight on an Arginine Synthesis Metabolon from the Tetrameric Structure of Yeast Acetylglutamate Kinase
Plos One, 7:34734-, 2012

PubMed Abstract: N-acetyl-L-glutamate kinase (NAGK) catalyzes the second, generally controlling, step of arginine biosynthesis. In yeasts, NAGK exists either alone or forming a metabolon with N-acetyl-L-glutamate synthase (NAGS), which catalyzes the first step and exists only within the metabolon. Yeast NAGK (yNAGK) has, in addition to the amino acid kinase (AAK) domain found in other NAGKs, a ~150-residue C-terminal domain of unclear significance belonging to the DUF619 domain family. We deleted this domain, proving that it stabilizes yNAGK, slows catalysis and modulates feed-back inhibition by arginine. We determined the crystal structures of both the DUF619 domain-lacking yNAGK, ligand-free as well as complexed with acetylglutamate or acetylglutamate and arginine, and of complete mature yNAGK. While all other known arginine-inhibitable NAGKs are doughnut-like hexameric trimers of dimers of AAK domains, yNAGK has as central structure a flat tetramer formed by two dimers of AAK domains. These dimers differ from canonical AAK dimers in the -110° rotation of one subunit with respect to the other. In the hexameric enzymes, an N-terminal extension, found in all arginine-inhibitable NAGKs, forms a protruding helix that interlaces the dimers. In yNAGK, however, it conforms a two-helix platform that mediates interdimeric interactions. Arginine appears to freeze an open inactive AAK domain conformation. In the complete yNAGK structure, two pairs of DUF619 domains flank the AAK domain tetramer, providing a mechanism for the DUF619 domain modulatory functions. The DUF619 domain exhibits the histone acetyltransferase fold, resembling the catalytic domain of bacterial NAGS. However, the putative acetyl CoA site is blocked, explaining the lack of NAGS activity of yNAGK. We conclude that the tetrameric architecture is an adaptation to metabolon formation and propose an organization for this metabolon, suggesting that yNAGK may be a good model also for yeast and human NAGSs.

PubMed: 22529931
DOI: 10.1371/JOURNAL.PONE.0034734

実験手法

X-RAY DIFFRACTION (3.25 Å)