Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 50.41 kDa 
• Atom Count: 3439 
• Modelled Residue Count: 387 
• Deposited Residue Count: 435 
• Unique protein chains: 2

5L8H

Structure of USP46-UbVME

• PDB DOI: 10.2210/pdb5L8H/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-06-07 Released: 2016-09-28 
• Deposition Author(s): Clerici, M., Sixma, T., Dharadhar, S.
• Funding Organization(s): KWF, ERC

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.194 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 

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

• PubMed: 27650958 
• DOI: 10.1016/j.jsb.2016.09.011
• Primary Citation of Related Structures:  
  5L8E, 5L8H, 5L8W


• 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 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.

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Organizational Affiliation: 

Division of Biochemistry and CGC.nl, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 46	A	359	Homo sapiens	Mutation(s): 0  Gene Names: USP46 EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for P62068 (Homo sapiens) Explore P62068  Go to UniProtKB:  P62068
PHAROS:  P62068 GTEx:  ENSG00000109189

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	B	76	Homo sapiens	Mutation(s): 1  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.194 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.95	α = 90
b = 104.66	β = 90
c = 135.31	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-06-07 
• Released Date: 2016-09-28 
Deposition Author(s): Clerici, M., Sixma, T., Dharadhar, S.

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Funding Organization	Location	Grant Number
KWF	Netherlands	NKI-2014-6858
KWF	Netherlands	NKI- 2008-4014
ERC	Netherlands	249997

Revision History  

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