NMR structure of ubiquitin-like domain of hHR23B

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 60 
  • Conformers Submitted: 14 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Binding surface mapping of intra- and interdomain interactions among hHR23B, ubiquitin, and polyubiquitin binding site 2 of S5a

Ryu, K.S.Lee, K.J.Bae, S.H.Kim, B.K.Kim, K.A.Choi, B.S.

(2003) J Biol Chem 278: 36621-36627

  • DOI: https://doi.org/10.1074/jbc.M304628200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    hHR23B is the human homologue of the yeast protein RAD23 and is known to participate in DNA repair by stabilizing xeroderma pigmentosum group C protein. However, hHR23B and RAD23 also have many important functions related to general proteolysis. hHR23B consists of N-terminal ubiquitin-like (UbL), ubiquitin association 1 (UBA1), xeroderma pigmentosum group C binding, and UBA2 domains. The UBA domains interact with ubiquitin (Ub) and inhibit the assembly of polyubiquitin. On the other hand, the UbL domain interacts with the poly-Ub binding site 2 (PUbS2) domain of the S5a protein, which can carry polyubiquitinated substrates into the proteasome. We calculated the NMR structure of the UbL domain of hHR23B and determined binding surfaces of UbL and Ub to UBA1, UBA2, of hHR23B and PUbS2 of S5a by using chemical shift perturbation. Interestingly, the surfaces of UbL and Ub that bind to UBA1, UBA2, and PUbS2 are similar, consisting of five beta-strands and their connecting loops. This is the first report that an intramolecular interaction between UbL and UBA domains is possible, and this interaction could be important for the control of proteolysis by hHR23B. The binding specificities of UbL and Ub for PUbS1, PUbS2, and general ubiquitin-interacting motifs, which share the LALA motif, were evaluated. The UBA domains bind to the surface of Ub including Lys-48, which is required for multiubiquitin assembly, possibly explaining the observed inhibition of multiubiquitination by hHR23B. The UBA domains bind to UbL through electrostatic interactions supported by hydrophobic interactions and to Ub mainly through hydrophobic interactions supported by electrostatic interactions.

  • Organizational Affiliation

    Yusong-Gu, Gusong-Dong 373-1, Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejon 305-701, South Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UV excision repair protein RAD23 homolog B85Homo sapiensMutation(s): 0 
Gene Names: hHR23B
UniProt & NIH Common Fund Data Resources
Find proteins for P54727 (Homo sapiens)
Explore P54727 
Go to UniProtKB:  P54727
PHAROS:  P54727
GTEx:  ENSG00000119318 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54727
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 60 
  • Conformers Submitted: 14 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-07-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-23
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-05-29
    Changes: Data collection