7DVF

Crystal structure of the computationally designed reDPBB_sym2 protein

7DVF の概要

• エントリーDOI: 10.2210/pdb7dvf/pdb
• 分子名称: reDPBB_sym2 protein, (4S)-2-METHYL-2,4-PENTANEDIOL (3 entities in total)
• 機能のキーワード: double psi beta barrel, chaperone
• 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: 9536.28

構造登録者

Yagi, S.,Tagami, S.,Padhi, A.K.,Zhang, K.Y.J. (登録日: 2021-01-13, 公開日: 2021-10-13, 最終更新日: 2023-11-29)

主引用文献

Yagi, S.,Padhi, A.K.,Vucinic, J.,Barbe, S.,Schiex, T.,Nakagawa, R.,Simoncini, D.,Zhang, K.Y.J.,Tagami, S.
Seven Amino Acid Types Suffice to Create the Core Fold of RNA Polymerase.
J.Am.Chem.Soc., 143:15998-16006, 2021

PubMed Abstract: The extant complex proteins must have evolved from ancient short and simple ancestors. The double-ψ β-barrel (DPBB) is one of the oldest protein folds and conserved in various fundamental enzymes, such as the core domain of RNA polymerase. Here, by reverse engineering a modern DPBB domain, we reconstructed its plausible evolutionary pathway started by "interlacing homodimerization" of a half-size peptide, followed by gene duplication and fusion. Furthermore, by simplifying the amino acid repertoire of the peptide, we successfully created the DPBB fold with only seven amino acid types (Ala, Asp, Glu, Gly, Lys, Arg, and Val), which can be coded by only GNN and ARR (R = A or G) codons in the modern translation system. Thus, the DPBB fold could have been materialized by the early translation system and genetic code.

PubMed: 34559526
DOI: 10.1021/jacs.1c05367

実験手法

X-RAY DIFFRACTION (1.209 Å)