2KDI

Solution structure of a Ubiquitin/UIM fusion protein

Summary for 2KDI

• Entry DOI: 10.2210/pdb2kdi/pdb
• NMR Information: BMRB: 16114
• Descriptor: Ubiquitin, Vacuolar protein sorting-associated protein 27 fusion protein (1 entity in total)
• Functional Keywords: ubiquitin, ubiquitin interacting motif, uim, protein domain interface, endosome, membrane, metal-binding, phosphoprotein, zinc, zinc-finger, signaling protein
• Biological source: Saccharomyces cerevisiae (yeast)
• Total number of polymer chains: 1
• Total formula weight: 12867.40

Authors

Sgourakis, N.G.,Patel, M.M.,Garcia, A.E.,Makhatadze, G.I.,McCallum, S.A. (deposition date: 2009-01-09, release date: 2010-02-09, Last modification date: 2024-05-08)

Primary citation

Sgourakis, N.G.,Patel, M.M.,Garcia, A.E.,Makhatadze, G.I.,McCallum, S.A.
Conformational Dynamics and Structural Plasticity Play Critical Roles in the Ubiquitin Recognition of a UIM Domain.
J.Mol.Biol., 396:1128-1144, 2010

PubMed Abstract: Ubiquitin-interacting motifs (UIMs) are an important class of protein domains that interact with ubiquitin or ubiquitin-like proteins. These approximately 20-residue-long domains are found in a variety of ubiquitin receptor proteins and serve as recognition modules towards intracellular targets, which may be individual ubiquitin subunits or polyubiquitin chains attached to a variety of proteins. Previous structural studies of interactions between UIMs and ubiquitin have shown that UIMs adopt an extended structure of a single alpha-helix, containing a hydrophobic surface with a conserved sequence pattern that interacts with key hydrophobic residues on ubiquitin. In light of this large body of structural studies, details regarding the presence and the roles of structural dynamics and plasticity are surprisingly lacking. In order to better understand the structural basis of ubiquitin-UIM recognition, we have characterized changes in the structure and dynamics of ubiquitin upon binding of a UIM domain from the yeast Vps27 protein. The solution structure of a ubiquitin-UIM fusion protein designed to study these interactions is reported here and found to consist of a well-defined ubiquitin core and a bipartite UIM helix. Moreover, we have studied the plasticity of the docking interface, as well as global changes in ubiquitin due to UIM binding at the picoseconds-to-nanoseconds and microseconds-to-milliseconds protein motions by nuclear magnetic resonance relaxation. Changes in generalized-order parameters of amide groups show a distinct trend towards increased structural rigidity at the UIM-ubiquitin interface relative to values determined in unbound ubiquitin. Analysis of (15)N Carr-Purcell-Meiboom-Gill relaxation dispersion measurements suggests the presence of two types of motions: one directly related to the UIM-binding interface and the other induced to distal parts of the protein. This study demonstrates a case where localized interactions among protein domains have global effects on protein motions at timescales ranging from picoseconds to milliseconds.

PubMed: 20053359
DOI: 10.1016/j.jmb.2009.12.052

Experimental method

SOLUTION NMR