6C2V

Solution structure of a phosphate-loop protein

6C2V の概要

• エントリーDOI: 10.2210/pdb6c2v/pdb
• 関連するPDBエントリー: 6C2U
• NMR情報: BMRB: 30395
• 分子名称: phosphate-loop protein (1 entity in total)
• 機能のキーワード: protein design, phosphate loop, ideal fold, grafting, de novo protein
• 由来する生物種: synthetic construct
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 12501.37

構造登録者

Yang, F.,Yang, W.,Lin, Y.R.,Romero Romero, M.L.,Tawfik, D.,Baker, D.,Varani, G. (登録日: 2018-01-09, 公開日: 2018-11-21, 最終更新日: 2024-05-15)

主引用文献

Romero Romero, M.L.,Yang, F.,Lin, Y.R.,Toth-Petroczy, A.,Berezovsky, I.N.,Goncearenco, A.,Yang, W.,Wellner, A.,Kumar-Deshmukh, F.,Sharon, M.,Baker, D.,Varani, G.,Tawfik, D.S.
Simple yet functional phosphate-loop proteins.
Proc. Natl. Acad. Sci. U.S.A., 115:E11943-E11950, 2018

PubMed Abstract: Abundant and essential motifs, such as phosphate-binding loops (P-loops), are presumed to be the seeds of modern enzymes. The Walker-A P-loop is absolutely essential in modern NTPase enzymes, in mediating binding, and transfer of the terminal phosphate groups of NTPs. However, NTPase function depends on many additional active-site residues placed throughout the protein's scaffold. Can motifs such as P-loops confer function in a simpler context? We applied a phylogenetic analysis that yielded a sequence logo of the putative ancestral Walker-A P-loop element: a β-strand connected to an α-helix via the P-loop. Computational design incorporated this element into de novo designed β-α repeat proteins with relatively few sequence modifications. We obtained soluble, stable proteins that unlike modern P-loop NTPases bound ATP in a magnesium-independent manner. Foremost, these simple P-loop proteins avidly bound polynucleotides, RNA, and single-strand DNA, and mutations in the P-loop's key residues abolished binding. Binding appears to be facilitated by the structural plasticity of these proteins, including quaternary structure polymorphism that promotes a combined action of multiple P-loops. Accordingly, oligomerization enabled a 55-aa protein carrying a single P-loop to confer avid polynucleotide binding. Overall, our results show that the P-loop Walker-A motif can be implemented in small and simple β-α repeat proteins, primarily as a polynucleotide binding motif.

PubMed: 30504143
DOI: 10.1073/pnas.1812400115

実験手法

SOLUTION NMR