8JVO

Crystal structure of the chemically synthesized mk2h_deltaMILPYS peptide homodimer, DZBB form

Summary for 8JVO

• Entry DOI: 10.2210/pdb8jvo/pdb
• Descriptor: mk2h_deltaMILPYS, SULFATE ION (3 entities in total)
• Functional Keywords: double zeta beta barrel, dna binding protein
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 4972.78

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

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: 39025855
DOI: 10.1038/s41467-024-50013-9

Experimental method

X-RAY DIFFRACTION (1.701 Å)