2FZP

Crystal structure of the USP8 interaction domain of human NRDP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Amino-terminal Dimerization, NRDP1-Rhodanese Interaction, and Inhibited Catalytic Domain Conformation of the Ubiquitin-specific Protease 8 (USP8).

Avvakumov, G.V.Walker, J.R.Xue, S.Finerty Jr., P.J.Mackenzie, F.Newman, E.M.Dhe-Paganon, S.

(2006) J Biol Chem 281: 38061-38070

  • DOI: 10.1074/jbc.M606704200
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Ubiquitin-specific protease 8 (USP8) hydrolyzes mono and polyubiquitylated targets such as epidermal growth factor receptors and is involved in clathrin-mediated internalization. In 1182 residues, USP8 contains multiple domains, including coiled-coil ...

    Ubiquitin-specific protease 8 (USP8) hydrolyzes mono and polyubiquitylated targets such as epidermal growth factor receptors and is involved in clathrin-mediated internalization. In 1182 residues, USP8 contains multiple domains, including coiled-coil, rhodanese, and catalytic domains. We report the first high-resolution crystal structures of these domains and discuss their implications for USP8 function. The amino-terminal domain is a homodimer with a novel fold. It is composed of two five-helix bundles, where the first helices are swapped, and carboxyl-terminal helices are extended in an antiparallel fashion. The structure of the rhodanese domain, determined in complex with the E3 ligase NRDP1, reveals the canonical rhodanese fold but with a distorted primordial active site. The USP8 recognition domain of NRDP1 has a novel protein fold that interacts with a conserved peptide loop of the rhodanese domain. A consensus sequence of this loop is found in other NRDP1 targets, suggesting a common mode of interaction. The structure of the carboxyl-terminal catalytic domain of USP8 exhibits the conserved tripartite architecture but shows unique traits. Notably, the active site, including the ubiquitin binding pocket, is in a closed conformation, incompatible with substrate binding. The presence of a zinc ribbon subdomain near the ubiquitin binding site further suggests a polyubiquitin-specific binding site and a mechanism for substrate induced conformational changes.


    Related Citations: 
    • Stabilization of the E3 ubiquitin ligase Nrdp1 by the deubiquitinating enzyme USP8.
      Wu, X., Yen, L., Irwin, L., Sweeney, C., Carraway, K.L.
      (2004) Mol Cell Biol 24: 7748
    • Nrdp1-mediated degradation of the gigantic IAP, BRUCE, is a novel pathway for triggering apoptosis.
      Qiu, X.B., Markant, S.L., Yuan, J., Goldberg, A.L.
      (2004) EMBO J 23: 800
    • An RBCC protein implicated in maintenance of steady-state neuregulin receptor levels.
      Diamonti, A.J., Guy, P.M., Ivanof, C., Wong, K., Sweeney, C., Carraway, K.L.
      (2002) Proc Natl Acad Sci U S A 99: 2866
    • FLRF, a novel evolutionarily conserved RING finger gene, is differentially expressed in mouse fetal and adult hematopoietic stem cells and progenitors.
      Abdullah, J.M., Li, X., Nachtman, R.G., Jurecic, R.
      (2001) Blood Cells Mol Dis 27: 320

    Organizational Affiliation

    Structural Genomics Consortium and the Department of Physiology, University of Toronto, Toronto, Ontario M5G 1L5, Canada.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ring finger protein 41 isoform 1
A
144Homo sapiensMutation(s): 0 
Gene Names: RNF41FLRFNRDP1SBBI03
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for Q9H4P4 (Homo sapiens)
Go to UniProtKB:  Q9H4P4
NIH Common Fund Data Resources
PHAROS  Q9H4P4
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.796α = 90
b = 44.262β = 90
c = 88.339γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
ARP/wARPmodel building

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2006-03-28
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance