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The UBX domain: a widespread ubiquitin-like module
A Buchberger1, M J Howard, M Proctor
1MRC Centre for Protein Engineering, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
Journal of Molecular Biology
|March 13, 2001
Summary
The UBX domain, found in eukaryotic proteins, shares a structural fold with ubiquitin. This structural similarity suggests a ubiquitin-related function, though direct conjugation is unlikely.
Area of Science:
- Structural biology
- Protein domains
- Biochemistry
Background:
- The UBX domain is an 80 amino acid module typically found at the carboxyl terminus of eukaryotic proteins.
- Understanding the function of UBX domains is crucial for comprehending protein regulation and cellular processes.
Purpose of the Study:
- To elucidate the function of UBX domains by determining the three-dimensional structure of the UBX domain from human Fas-associated factor-1 (FAF1).
Main Methods:
- Nuclear Magnetic Resonance (NMR) spectroscopy was used to solve the three-dimensional structure of the FAF1 UBX domain.
- Structural comparison with ubiquitin was performed using root-mean-square deviation (r.m.s.d.) analysis.
Main Results:
- The FAF1 UBX domain adopts a beta-Grasp fold with a specific secondary structure organization (beta-beta-alpha-beta-beta-alpha-beta).
- The UBX domain superimposes with ubiquitin (r.m.s.d. of 1.9 A), indicating a shared superfold and potential evolutionary relationship.
- Key features for ubiquitin conjugation (carboxyl-terminal extension with double glycine motif, suitably positioned lysines) are absent, making direct conjugation unlikely.
Conclusions:
- The UBX domain shares a structural fold with ubiquitin, suggesting a role in ubiquitin-related processes.
- Most UBX domain-containing proteins belong to evolutionarily conserved families (FAF1, p47, Y33K, Rep8).
- Direct conjugation of UBX domains to other proteins or involvement in mixed UBX-ubiquitin chains is improbable.