7DG7
DPBB domain of VCP-like ATPase from Methanopyrus kandleri
Summary for 7DG7
| Entry DOI | 10.2210/pdb7dg7/pdb |
| Descriptor | ATPase of the AAA+ class, IMIDAZOLE, ZINC ION, ... (4 entities in total) |
| Functional Keywords | double psi beta barrel, chaperone |
| Biological source | Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938) |
| Total number of polymer chains | 1 |
| Total formula weight | 10654.97 |
| Authors | Yagi, S.,Tagami, S. (deposition date: 2020-11-11, release date: 2021-09-29, Last modification date: 2024-05-29) |
| 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 Cited by 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: 34559526DOI: 10.1021/jacs.1c05367 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.604 Å) |
Structure validation
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