2WYQ

THE CRYSTAL STRUCTURE OF THE UBIQUITIN-LIKE (UBL) DOMAIN OF HHR23A (HUMAN HOMOLOGUE A OF RAD23)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.126 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Crystal Structure of the Ubiquitin-Like (Ubl) Domain of Human Homologue a of Rad23 (Hhr23A) Protein

Chen, Y.W.Tajima, T.Agrawal, S.

(2011) Protein Eng Des Sel 24: 131

  • DOI: 10.1093/protein/gzq084
  • Primary Citation of Related Structures:  
    2WYQ

  • PubMed Abstract: 
  • The human homologue of the yeast Rad23 protein, hHR23A, plays dual roles in DNA repair as well as in translocating polyubiquitinated proteins to the proteasome. We determined the three-dimensional structure of its ubiquitin-like (UbL) domain by X-ray cry ...

    The human homologue of the yeast Rad23 protein, hHR23A, plays dual roles in DNA repair as well as in translocating polyubiquitinated proteins to the proteasome. We determined the three-dimensional structure of its ubiquitin-like (UbL) domain by X-ray crystallography. It has the same overall structure and fold characteristics as ubiquitin and other members of the UbL domain family, with overall root mean square deviations in Cα positions in the range of 1.0-1.3 Å. There are local differences in the α1-β3 loop where hHR23A UbL domain has three more residues constituting a bigger loop. Analysis of the crystal packing revealed a possible dimeric arrangement mediated by the three residues (Leu10, Ile49 and Met75) that are known to be critical for molecular interactions. In contrast to the overall well-defined structure, these three residues are either disordered or have multiple conformations, suggesting that conformation variability is an important property of the binding surface. The electrostatic potentials at the binding surface are conserved among the family, with the hHR23B domain being the most similar to this structure. The intra-molecular complexes formed by the UbL domain of hHR23A with its UbA1 or UbA2 domains was studied by comparative homology modelling, which suggests these two interactions are structurally similar and are mutually exclusive.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Diffraction Studies of the Ubiquitin-Like (Ubl) Domain of the Human Homologue a of Rad23 (Hhr23A) Protein.
      Chen, Y.W., Tajima, T., Rees, M., Garcia-Maya, M.
      (2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 930
    • Structural Determinants for the Binding of Ubiquitin-Like Domains to the Proteasome.
      Mueller, T.D., Feigon, J.
      (2003) EMBO J 22: 4634
    • DNA-Repair Protein Hhr23A Alters its Protein Structure Upon Binding Proteasomal Subunit S5A.
      Walters, K.J., Lech, P.J., Goh, A.M., Wang, Q., Howley, P.M.
      (2003) Proc Natl Acad Sci U S A 100: 12694

    Organizational Affiliation

    King's College London, Randall Division of Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, London SE11UL, UK. yu-wai.chen@kcl.ac.uk



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UV EXCISION REPAIR PROTEIN RAD23 HOMOLOG A A85Homo sapiensMutation(s): 0 
Gene Names: RAD23A
Find proteins for P54725 (Homo sapiens)
Explore P54725 
Go to UniProtKB:  P54725
NIH Common Fund Data Resources
PHAROS:  P54725
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.126 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.434α = 90
b = 78.434β = 90
c = 63.472γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2009-11-19 
  • Released Date: 2010-11-10 
  • Deposition Author(s): Chen, Y.W.

Revision History 

  • Version 1.0: 2010-11-10
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance