5L8W

Structure of USP12-UB-PRG/UAF1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A conserved two-step binding for the UAF1 regulator to the USP12 deubiquitinating enzyme.

Dharadhar, S.Clerici, M.van Dijk, W.J.Fish, A.Sixma, T.K.

(2016) J.Struct.Biol. 196: 437-447

  • DOI: 10.1016/j.jsb.2016.09.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Regulation of deubiquitinating enzyme (DUB) activity is an essential step for proper function of cellular ubiquitin signals. UAF1 is a WD40 repeat protein, which binds and activates three important DUBs, USP1, USP12 and USP46. Here, we report the cry ...

    Regulation of deubiquitinating enzyme (DUB) activity is an essential step for proper function of cellular ubiquitin signals. UAF1 is a WD40 repeat protein, which binds and activates three important DUBs, USP1, USP12 and USP46. Here, we report the crystal structure of the USP12-Ub/UAF1 complex at a resolution of 2.8Å and of UAF1 at 2.3Å. In the complex we find two potential sites for UAF1 binding, analogous to what was seen in a USP46/UAF1 complex. In line with these observed dual binding states, we show here that USP12/UAF1 complex has 1:2 stoichiometry in solution, with a two-step binding at 4nM and 325nM respectively. Mutagenesis studies show that the fingers sub-domain of USP12 interacts with UAF1 to form the high affinity interface. Our activation studies confirm that the high affinity binding is important for activation while the second UAF1 binding does not affect activation. Nevertheless, we show that this two step binding is conserved in the well-studied USP12 paralog, USP1. Our results highlight the interfaces essential for regulation of USP12 activity and show a conserved second binding of UAF1 which could be important for regulatory functions independent of USP12 activity.


    Organizational Affiliation

    Division of Biochemistry and CGC.nl, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.,Division of Biochemistry and CGC.nl, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands. Electronic address: t.sixma@nki.nl.,Division of Biochemistry and CGC.nl, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands; Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin carboxyl-terminal hydrolase 12
A
376Homo sapiensMutation(s): 0 
Gene Names: USP12 (UBH1, USP12L1)
EC: 3.4.19.12
Find proteins for O75317 (Homo sapiens)
Go to Gene View: USP12
Go to UniProtKB:  O75317
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
WD repeat-containing protein 48
B
580Homo sapiensMutation(s): 0 
Gene Names: WDR48 (KIAA1449, UAF1)
Find proteins for Q8TAF3 (Homo sapiens)
Go to Gene View: WDR48
Go to UniProtKB:  Q8TAF3
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-B
C
75Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Small Molecules
Ligands 3 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
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
AYE
Query on AYE

Download SDF File 
Download CCD File 
A
prop-2-en-1-amine
ALLYLAMINE
C3 H7 N
VVJKKWFAADXIJK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.208 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 103.679α = 90.00
b = 152.820β = 90.00
c = 182.932γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
KWFNetherlandsNKI-2014-6858
KWFNetherlandsNKI 2008-4014
ERCNetherlands249997

Revision History 

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2016-11-30
    Type: Database references