1Z96

Crystal structure of the Mud1 UBA domain

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Mechanism of Lys48-linked polyubiquitin chain recognition by the Mud1 UBA domain

Trempe, J.-F., Brown, N.R., Lowe, E.D., Gordon, C., Campbell, I.D., Noble, M.E.M., Endicott, J.A.

(2005) Embo J. 24: 3178-3189

  • DOI: 10.1038/sj.emboj.7600797

  • 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 polyubiquiti ...

    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.

    Organizational Affiliation: 

    Laboratory of Molecular Biophysics, University of Oxford, Oxford, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UBA-domain protein mud1
A, B
40Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: mud1 (ddi1, ucp1)
EC: 3.4.23.-
Find proteins for Q10256 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q10256
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.167 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 60.601α = 90.00
b = 60.601β = 90.00
c = 96.350γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
CCP4data scaling
SHELXDphasing
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-04
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance