5K1A

Crystal structure of the UAF1-USP12 complex in C2 space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Allosteric Activation of Ubiquitin-Specific Proteases by beta-Propeller Proteins UAF1 and WDR20.

Li, H.Lim, K.S.Kim, H.Hinds, T.R.Jo, U.Mao, H.Weller, C.E.Sun, J.Chatterjee, C.D'Andrea, A.D.Zheng, N.

(2016) Mol.Cell 63: 249-260

  • DOI: 10.1016/j.molcel.2016.05.031
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ubiquitin-specific proteases (USPs) constitute the largest family of deubiquitinating enzymes, whose catalytic competency is often modulated by their binding partners through unknown mechanisms. Here we report on a series of crystallographic and bioc ...

    Ubiquitin-specific proteases (USPs) constitute the largest family of deubiquitinating enzymes, whose catalytic competency is often modulated by their binding partners through unknown mechanisms. Here we report on a series of crystallographic and biochemical analyses of an evolutionarily conserved deubiquitinase, USP12, which is activated by two β-propeller proteins, UAF1 and WDR20. Our structures reveal that UAF1 and WDR20 interact with USP12 at two distinct sites far from its catalytic center. Without increasing the substrate affinity of USP12, the two β-propeller proteins potentiate the enzyme through different allosteric mechanisms. UAF1 docks at the distal end of the USP12 Fingers domain and induces a cascade of structural changes that reach a critical ubiquitin-contacting loop adjacent to the catalytic cleft. By contrast, WDR20 anchors at the base of this loop and remotely modulates the catalytic center of the enzyme. Our results provide a mechanistic example for allosteric activation of USPs by their regulatory partners.


    Organizational Affiliation

    Department of Pharmacology, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Box 357280, University of Washington, Seattle, WA 98195, USA.,Department of Pharmacology, University of Washington, Seattle, WA 98195, USA.,Department of Pharmacology, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Box 357280, University of Washington, Seattle, WA 98195, USA. Electronic address: nzheng@uw.edu.,Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA.,Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.,Department of Chemistry, University of Washington, Seattle, WA 98195, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin carboxyl-terminal hydrolase 12
A, C, E, G
331Homo 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, D, F, H
677Homo sapiensMutation(s): 0 
Gene Names: WDR48 (KIAA1449, UAF1)
Find proteins for Q8TAF3 (Homo sapiens)
Go to Gene View: WDR48
Go to UniProtKB:  Q8TAF3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 262.425α = 90.00
b = 103.301β = 117.47
c = 178.466γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History 

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2016-08-10
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2019-11-20
    Type: Author supporting evidence