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
  • Primary Citation of Related Structures:  
    1Q5W

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
homolog of yeast nuclear protein localization 4A31Rattus norvegicusMutation(s): 0 
Gene Names: Npl4Nploc4
Find proteins for Q9ES54 (Rattus norvegicus)
Explore Q9ES54 
Go to UniProtKB:  Q9ES54
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinB76Homo sapiensMutation(s): 0 
Gene Names: (UBA52 OR UBCEP2) AND UBB AND UBC AND (UBA80 OR UBCEP1 OR RPS27A)UBC
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
NIH Common Fund Data Resources
PHAROS  P0CG48
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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



Entry History 

Deposition Data

Revision History 

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