32UY

Protein with 8.3 knot

Summary for 32UY

• Entry DOI: 10.2210/pdb32uy/pdb
• Descriptor: Protein with 8.3 knot, 1,2-ETHANEDIOL, SULFATE ION, ... (5 entities in total)
• Functional Keywords: 8.3 knot, novel fold, eight fold, lachnospiraceae bacterium, unknown function
• Biological source: Lachnospiraceae bacterium
• Total number of polymer chains: 2
• Total formula weight: 108885.19

Authors

Mozajew, M.,Kluza, A.,Sulkowska, J.I. (deposition date: 2026-07-27, release date: 2026-10-21, Last modification date: 2026-10-28)

Primary citation

Mozajew, M.,Sikora, M.,Fortunka, M.,Perlinska, A.P.,Kluza, A.,Niewieczerzal, S.,da Silva, F.B.,Lukaszewicz, M.,Sikorska, J.A.,Mikulska, L.J.,Jackson, S.E.,Sulkowska, J.I.
Unique features of EIGHT fold-Proteins with the most complex 8 3 knotted topology.
Proc.Natl.Acad.Sci.USA, 123:e2523017123-e2523017123, 2026

PubMed Abstract: Herein, we present three crystal structures of the most complex knotted protein to date, an [Formula: see text] knot with eight crossings, which belongs to a clasp knot family. The fold of this protein is also unique, and we call it the EIGHT fold (Extraordinarily Intricate Globular Helical Tangled fold). The [Formula: see text] knot is found only in a certain group of bacteria, where it is strictly conserved, despite sequence identities as low as 10%. The [Formula: see text] structure shows a high level of internal symmetry, with structurally analogous halves. It is possible that the EIGHT fold evolved from a single unknotted "half" that duplicated and formed a complex protein. Based on an in vitro study of three selected [Formula: see text] proteins, we estimated their thermal and thermodynamic stability, and showed that they follow a two-state unfolding model under equilibrium conditions and their refolding occurs to a compact, nonnative state. Unfolding kinetics of [Formula: see text] knotted proteins reveal a complex, multiphase process spanning milliseconds to days. Six kinetic phases were resolved using stopped-flow fluorescence and far-ultraviolet absorbance circular dichroism spectroscopy, highlighting both rapid early events and slower rearrangements in secondary and tertiary structures. Finally, with a structure-based model, we showed that proteins with an [Formula: see text] knot can self-tie through a [Formula: see text] knotted intermediate state. They can also self-untie, albeit via an additional intermediate knot such as [Formula: see text]. Nevertheless, these proteins do not seem to fit with current folding theories known to date and require the development of a new approach.

PubMed: 42896058
DOI: 10.1073/pnas.2523017123

Experimental method

X-RAY DIFFRACTION (2.54 Å)