3DGN

A non-biological ATP binding protein crystallized in the presence of 100 mM ADP

3DGN の概要

• エントリーDOI: 10.2210/pdb3dgn/pdb
• 関連するPDBエントリー: 2P05 2P09 3DGL 3DGM 3DGO
• 分子名称: ATP Binding Protein-DX, ZINC ION, ADENOSINE-5'-DIPHOSPHATE, ... (5 entities in total)
• 機能のキーワード: alpha/beta fold, bent atp, non-biological protein, de novo protein
• 由来する生物種: unidentified
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 10412.96

構造登録者

Simmons, C.R.,Allen, J.P.,Chaput, J.C. (登録日: 2008-06-13, 公開日: 2009-06-30, 最終更新日: 2024-02-21)

主引用文献

Simmons, C.R.,Stomel, J.M.,McConnell, M.D.,Smith, D.A.,Watkins, J.L.,Allen, J.P.,Chaput, J.C.
A synthetic protein selected for ligand binding affinity mediates ATP hydrolysis.
Acs Chem.Biol., 4:649-658, 2009

PubMed Abstract: How primitive enzymes emerged from a primordial pool remains a fundamental unanswered question with important practical implications in synthetic biology. Here we show that a de novo evolved ATP binding protein, selected solely on the basis of its ability to bind ATP, mediates the regiospecific hydrolysis of ATP to ADP when crystallized with 1 equiv of ATP. Structural insights into this reaction were obtained by growing protein crystals under saturating ATP conditions. The resulting crystal structure refined to 1.8 A resolution reveals that this man-made protein binds ATP in an unusual bent conformation that is metal-independent and held in place by a key bridging water molecule. Removal of this interaction using a null mutant results in a variant that binds ATP in a normal linear geometry and is incapable of ATP hydrolysis. Biochemical analysis, including high-resolution mass spectrometry performed on dissolved protein crystals, confirms that the reaction is accelerated in the crystalline environment. This observation suggests that proteins with weak chemical reactivity can emerge from high affinity ligand binding sites and that constrained ligand-binding geometries could have helped to facilitate the emergence of early protein enzymes.

PubMed: 19522480
DOI: 10.1021/cb900109w

実験手法

X-RAY DIFFRACTION (2.7 Å)