NMR solution structure of the ubiquitin conjugating enzyme UbcH5B

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 10 
  • Selection Criteria: LOWEST ENERGY 

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Solution Structure of the Ubiquitin-Conjugating Enzyme Ubch5B

Houben, K.Dominguez, C.Van Schaik, F.M.A.Timmers, H.T.M.Bonvin, A.M.J.J.Boelens, R.

(2004) J Mol Biol 344: 513

  • DOI: https://doi.org/10.1016/j.jmb.2004.09.054
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The ubiquitination pathway is the main pathway for protein degradation in eukaryotic cells. The attachment of ubiquitin to a substrate protein is catalyzed by three types of enzymes, namely a ubiquitin activating enzyme (E1), a ubiquitin-conjugating enzyme (E2), and a ubiquitin ligase (E3). Here, the structure of the human ubiquitin-conjugating enzyme (E2) UbcH5B has been solved by a combination of homology modeling, NMR relaxation data and automated NOE assignments. Comparison to E2 structures solved previously by X-ray crystallography or NMR shows in all cases the same compact fold, but differences are observed in the orientation of both N and C-terminal alpha-helices. The N-terminal helix that is involved in binding to ubiquitin ligases (E3) displays a different position, which could have consequences for precise E2-E3 recognition. In addition, multiple conformations of the side-chain of Asn77 are found in solution, which contrasts the single hydrogen-bonded conformation in the crystal structures of E2 enzymes. The possible implication of this conformational freedom of Asn77 for its catalytic function is discussed.

  • Organizational Affiliation

    Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2147Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62837 (Homo sapiens)
Explore P62837 
Go to UniProtKB:  P62837
PHAROS:  P62837
GTEx:  ENSG00000131508 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62837
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 10 
  • Selection Criteria: LOWEST ENERGY 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-11-10
    Type: Initial release
  • Version 1.1: 2017-04-19
    Changes: Atomic model, Other