8JVQ
Crystal structure of the dimeric RIFT fold protein Ph1_DG
Summary for 8JVQ
| Entry DOI | 10.2210/pdb8jvq/pdb |
| Descriptor | Ph1_DG, SULFATE ION, CITRIC ACID, ... (4 entities in total) |
| Functional Keywords | rift barrel, dna binding protein |
| Biological source | synthetic construct |
| Total number of polymer chains | 1 |
| Total formula weight | 4969.88 |
| Authors | Yagi, S.,Tagami, S. (deposition date: 2023-06-28, release date: 2024-07-03, Last modification date: 2024-08-07) |
| Primary citation | Yagi, S.,Tagami, S. An ancestral fold reveals the evolutionary link between RNA polymerase and ribosomal proteins. Nat Commun, 15:5938-5938, 2024 Cited by PubMed Abstract: Numerous molecular machines are required to drive the central dogma of molecular biology. However, the means by which these numerous proteins emerged in the early evolutionary stage of life remains enigmatic. Many of them possess small β-barrel folds with different topologies, represented by double-psi β-barrels (DPBBs) conserved in DNA and RNA polymerases, and similar but topologically distinct six-stranded β-barrel RIFT or five-stranded β-barrel folds such as OB and SH3 in ribosomal proteins. Here, we discover that the previously reconstructed ancient DPBB sequence could also adopt a β-barrel fold named Double-Zeta β-barrel (DZBB), as a metamorphic protein. The DZBB fold is not found in any modern protein, although its structure shares similarities with RIFT and OB. Indeed, DZBB could be transformed into them through simple engineering experiments. Furthermore, the OB designs could be further converted into SH3 by circular-permutation as previously predicted. These results indicate that these β-barrels diversified quickly from a common ancestor at the beginning of the central dogma evolution. PubMed: 39025855DOI: 10.1038/s41467-024-50013-9 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.401 Å) |
Structure validation
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