1Z96

Crystal structure of the Mud1 UBA domain

Summary for 1Z96

• Entry DOI: 10.2210/pdb1z96/pdb
• Descriptor: UBA-domain protein mud1 (2 entities in total)
• Functional Keywords: uba, ubiquitin, three-helix bundle, protein transport
• Biological source: Schizosaccharomyces pombe (fission yeast)
• Total number of polymer chains: 2
• Total formula weight: 8121.04

Authors

Trempe, J.-F.,Brown, N.R.,Lowe, E.D.,Noble, M.E.M.,Gordon, C.,Campbell, I.D.,Johnson, L.N.,Endicott, J.A. (deposition date: 2005-03-31, release date: 2005-10-04, Last modification date: 2024-02-14)

Primary citation

Trempe, J.-F.,Brown, N.R.,Lowe, E.D.,Gordon, C.,Campbell, I.D.,Noble, M.E.M.,Endicott, J.A.
Mechanism of Lys48-linked polyubiquitin chain recognition by the Mud1 UBA domain
Embo J., 24:3178-3189, 2005

PubMed Abstract: The ubiquitin-pathway associated (UBA) domain is a 40-residue polyubiquitin-binding motif. The Schizosaccharomyces pombe protein Mud1 is an ortholog of the Saccharomyces cerevisiae DNA-damage response protein Ddi1 and binds to K48-linked polyubiquitin through its UBA domain. We have solved the crystal structure of Mud1 UBA at 1.8 angstroms resolution, revealing a canonical three-helical UBA fold. We have probed the interactions of this domain using mutagenesis, surface plasmon resonance, NMR and analytical ultracentrifugation. We show that the ubiquitin-binding surface of Mud1 UBA extends beyond previously recognized motifs and can be functionally dissected into primary and secondary ubiquitin-binding sites. Mutation of Phe330 to alanine, a residue exposed between helices 2 and 3, significantly reduces the affinity of the Mud1 UBA domain for K48-linked polyubiquitin, despite leaving the primary binding surface functionally intact. Moreover, K48-linked diubiquitin binds a single Mud1 UBA domain even in the presence of excess UBA. We therefore propose a mechanism for the recognition of K48-linked polyubiquitin chains by Mud1 in which diubiquitin units are specifically recognized by a single UBA domain.

PubMed: 16138082
DOI: 10.1038/sj.emboj.7600797

Experimental method

X-RAY DIFFRACTION (1.8 Å)