Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 8.12 kDa 
• Atom Count: 664 
• Residue Count: 80 
• Unique protein chains: 1

1Z96

Crystal structure of the Mud1 UBA domain

• DOI: 10.2210/pdb1Z96/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Schizosaccharomyces pombe
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-03-31 Released: 2005-10-04 
• Deposition Author(s): Trempe, J.-F., Brown, N.R., Lowe, E.D., Noble, M.E.M., Gordon, C., Campbell, I.D., Johnson, L.N., Endicott, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.196 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 

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

• PubMed: 16138082 
• DOI: 10.1038/sj.emboj.7600797
• Primary Citation of Related Structures:  
  1Z96


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UBA-domain protein mud1	A, B	40	Schizosaccharomyces pombe	Mutation(s): 0  Gene Names: mud1 EC: 3.4.23
Find proteins for Q10256 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q10256  Go to UniProtKB:  Q10256

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.196 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.601	α = 90
b = 60.601	β = 90
c = 96.35	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHELXD	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-03-31 
• Released Date: 2005-10-04 
Deposition Author(s): Trempe, J.-F., Brown, N.R., Lowe, E.D., Noble, M.E.M., Gordon, C., Campbell, I.D., Johnson, L.N., Endicott, J.A.

Revision History 

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