5K1C

Crystal structure of the UAF1/WDR20/USP12 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


This is version 1.1 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:  
    5K16, 5K19, 5K1A, 5K1B, 5K1C

  • 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 biochemical analyses of an evolutionarily conserved deubiquitinase, USP12, which is activated by two β-propeller proteins, UAF1 and WDR20 ...

    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. Electronic address: nzheng@uw.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 12A355Homo sapiensMutation(s): 0 
Gene Names: USP12UBH1USP12L1
EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for O75317 (Homo sapiens)
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Go to UniProtKB:  O75317
PHAROS:  O75317
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
WD repeat-containing protein 48B563Homo sapiensMutation(s): 0 
Gene Names: WDR48KIAA1449UAF1
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Find proteins for Q8TAF3 (Homo sapiens)
Explore Q8TAF3 
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PHAROS:  Q8TAF3
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
WD repeat-containing protein 20C569Homo sapiensMutation(s): 0 
Gene Names: WDR20
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TBZ3 (Homo sapiens)
Explore Q8TBZ3 
Go to UniProtKB:  Q8TBZ3
PHAROS:  Q8TBZ3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TAM
Query on TAM

Download Ideal Coordinates CCD File 
F [auth C]TRIS(HYDROXYETHYL)AMINOMETHANE
C7 H17 N O3
GKODZWOPPOTFGA-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 217.903α = 90
b = 217.903β = 90
c = 223.819γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Cootmodel building
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2016-08-10
    Changes: Database references