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 

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
  • Primary Citation of Related Structures:  
  • Also Cited By: 3N3K

  • 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: 
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    • 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.
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    • 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
    • Stabilization of the E3 ubiquitin ligase Nrdp1 by the deubiquitinating enzyme USP8.
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      (2004) Mol.Cell.Biol. 24: 7748


    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: RNF41 (FLRF, NRDP1)
EC: 2.3.2.27
Find proteins for Q9H4P4 (Homo sapiens)
Go to Gene View: RNF41
Go to UniProtKB:  Q9H4P4
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 34.796α = 90.00
b = 44.262β = 90.00
c = 88.339γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
ARP/wARPmodel building
PHASERphasing
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

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