7DI0

Crystal structure of the rationally designed apDPBB_sym_79 protein

Summary for 7DI0

• Entry DOI: 10.2210/pdb7di0/pdb
• Descriptor: apDPBB_sym_79 protein, SULFATE ION (3 entities in total)
• Functional Keywords: double psi beta barrel, chaperone
• Biological source: synthetic construct
• Total number of polymer chains: 3
• Total formula weight: 31893.67

Authors

Yagi, S.,Tagami, S. (deposition date: 2020-11-18, release date: 2021-09-29, Last modification date: 2023-11-29)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.6 Å)