1Q5W

Ubiquitin Recognition by Npl4 Zinc-Fingers


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations,structures with the lowest energy,target function 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Ubiquitin interactions of NZF zinc fingers.

Alam, S.L.Sun, J.Payne, M.Welch, B.D.Blake, B.K.Davis, D.R.Meyer, H.H.Emr, S.D.Sundquist, W.I.

(2004) Embo J. 23: 1411-1421

  • DOI: 10.1038/sj.emboj.7600114

  • PubMed Abstract: 
  • Ubiquitin (Ub) functions in many different biological pathways, where it typically interacts with proteins that contain modular Ub recognition domains. One such recognition domain is the Npl4 zinc finger (NZF), a compact zinc-binding module found in ...

    Ubiquitin (Ub) functions in many different biological pathways, where it typically interacts with proteins that contain modular Ub recognition domains. One such recognition domain is the Npl4 zinc finger (NZF), a compact zinc-binding module found in many proteins that function in Ub-dependent processes. We now report the solution structure of the NZF domain from Npl4 in complex with Ub. The structure reveals that three key NZF residues (13TF14/M25) surrounding the zinc coordination site bind the hydrophobic 'Ile44' surface of Ub. Mutations in the 13TF14/M25 motif inhibit Ub binding, and naturally occurring NZF domains that lack the motif do not bind Ub. However, substitution of the 13TF14/M25 motif into the nonbinding NZF domain from RanBP2 creates Ub-binding activity, demonstrating the versatility of the NZF scaffold. Finally, NZF mutations that inhibit Ub binding by the NZF domain of Vps36/ESCRT-II also inhibit sorting of ubiquitylated proteins into the yeast vacuole. Thus, the NZF is a versatile protein recognition domain that is used to bind ubiquitylated proteins during vacuolar protein sorting, and probably many other biological processes.


    Related Citations: 
    • Structure and ubiquitin interactions of the conserved zinc finger domain of Npl4.
      Wang, B.,Alam, S.L.,Meyer, H.H.,Payne, M.,Stemmler, T.L.,Davis, D.R.,Sundquist, W.I.
      (2003) J.Biol.Chem. 278: 20225


    Organizational Affiliation

    Department of Biochemistry, University of Utah, Salt Lake City, UT, USA. alam@wsu.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
homolog of yeast nuclear protein localization 4
A
31Rattus norvegicusMutation(s): 0 
Gene Names: Nploc4 (Npl4)
Find proteins for Q9ES54 (Rattus norvegicus)
Go to UniProtKB:  Q9ES54
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
B
76Homo sapiensMutation(s): 0 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  P0CG48
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations,structures with the lowest energy,target function 
  • Olderado: 1Q5W Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-30
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance