Solution Structure of Ubp-M Znf-UBP domain

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with favorable non-bond energy 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Solution structure of the Ubp-M BUZ domain, a highly specific protein module that recognizes the C-terminal tail of free ubiquitin.

Pai, M.T.Tzeng, S.R.Kovacs, J.J.Keaton, M.A.Li, S.S.Yao, T.P.Zhou, P.

(2007) J Mol Biol 370: 290-302

  • DOI: https://doi.org/10.1016/j.jmb.2007.04.015
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The BUZ/Znf-UBP domain is a distinct ubiquitin-binding module found in the cytoplasmic deacetylase HDAC6, the E3 ubiquitin ligase BRAP2/IMP, and a subfamily of deubiquitinating enzymes. Here, we report the solution structure of the BUZ domain of Ubp-M, a ubiquitin-specific protease, and its interaction with ubiquitin. Unlike the BUZ domain from isopeptidase T (isoT) that contains a single zinc finger, the Ubp-M BUZ domain features three zinc-binding sites consisting of 12 residues. These zinc ligands form a pair of cross-braced ring fingers encapsulated within a third zinc finger in the primary structure. In contrast to isoT, which can form an N-terminal loop swapped dimer in the crystal state, the formation of additional zinc fingers in the Ubp-M BUZ domain restricts its N-terminal loop to intra-domain interactions. The ubiquitin-binding site of the Ubp-M BUZ domain is mapped to the highly conserved, concave surface formed by the alpha 3 helix and the central beta-sheet. We further show that this site binds to the C-terminal tail of free ubiquitin, and corresponding peptides display essentially the same binding affinities as full-length ubiquitin does for the Ubp-M BUZ domain. However, modification of the G76(Ub) carboxylate group either by a peptide or isopeptide bond abolishes BUZ-domain interaction. The unique ubiquitin-recognition mode of the BUZ domain family suggests that they may function as "sensors" of free ubiquitin in cells to achieve regulatory roles in many aspects of ubiquitin-dependent processes.

  • Organizational Affiliation

    Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 16126Homo sapiensMutation(s): 0 
Gene Names: USP16
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5T5 (Homo sapiens)
Explore Q9Y5T5 
Go to UniProtKB:  Q9Y5T5
GTEx:  ENSG00000156256 
Entity Groups  
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UniProt GroupQ9Y5T5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with favorable non-bond energy 

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

  • Released Date: 2007-08-07 
  • Deposition Author(s): Pai, M.-T.

Revision History  (Full details and data files)

  • Version 1.0: 2007-08-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2022-03-09
    Changes: Database references, Derived calculations
  • Version 1.3: 2024-05-29
    Changes: Data collection