9IFR

CLIPPER domain from the Gram-negative fibrillar adhesin "B9T28_05395

Summary for 9IFR

• Entry DOI: 10.2210/pdb9ifr/pdb
• Descriptor: OmpA-like domain-containing protein, ACETATE ION (3 entities in total)
• Functional Keywords: fibrillar adhesin, adhesin, isopeptide bond, intramolecular isopeptide bond, cell adhesion
• Biological source: Acinetobacter silvestris
• Total number of polymer chains: 1
• Total formula weight: 12500.89

Authors

Barringer, R. (deposition date: 2025-02-18, release date: 2025-11-26)

Primary citation

Costa, F.,Riziotis, I.,Andreeva, A.,Kalwan, D.,de Jong, J.,Hinchliffe, P.,Parmeggiani, F.,Race, P.R.,Burston, S.G.,Bateman, A.,Barringer, R.
A global survey of intramolecular isopeptide bonds.
Protein Sci., 34:e70342-e70342, 2025

PubMed Abstract: Many proteins harbor covalent intramolecular bonds that enhance their stability and resistance to thermal, mechanical, and proteolytic insults. Intramolecular isopeptide bonds represent one such covalent interaction, yet their distribution across protein domains and organisms has been largely unexplored. Here, we sought to address this by employing a large-scale prediction of intramolecular isopeptide bonds in the AlphaFold database using the structural template-based software Isopeptor. Our findings reveal an extensive phyletic distribution in bacterial and archaeal surface proteins resembling fibrillar adhesins and pilins. All identified intramolecular isopeptide bonds are found in two structurally distinct folds, CnaA-like or CnaB-like, from a relatively small set of related Pfam families, including 10 novel families that we predict to contain intramolecular isopeptide bonds. One CnaA-like domain of unknown function, DUF11 (renamed here to "CLIPPER") is broadly distributed in cell-surface proteins from Gram-positive bacteria, Gram-negative bacteria, and archaea, and is structurally and biophysically characterized in this work. Using x-ray crystallography, we resolve a CLIPPER domain from a Gram-negative fibrillar adhesin that contains an intramolecular isopeptide bond and further demonstrate that it imparts thermostability and resistance to proteolysis. Our findings demonstrate the extensive distribution of intramolecular isopeptide bond-containing protein domains in nature and structurally resolve the previously cryptic CLIPPER domain.

PubMed: 41236442
DOI: 10.1002/pro.70342

Experimental method

X-RAY DIFFRACTION (1.77 Å)