5LRX

Structure of A20 OTU domain bound to ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular basis of Lys11-polyubiquitin specificity in the deubiquitinase Cezanne.

Mevissen, T.E.Kulathu, Y.Mulder, M.P.Geurink, P.P.Maslen, S.L.Gersch, M.Elliott, P.R.Burke, J.E.van Tol, B.D.Akutsu, M.El Oualid, F.Kawasaki, M.Freund, S.M.Ovaa, H.Komander, D.

(2016) Nature 538: 402-405

  • DOI: 10.1038/nature19836
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The post-translational modification of proteins with polyubiquitin regulates virtually all aspects of cell biology. Eight distinct chain linkage types co-exist in polyubiquitin and are independently regulated in cells. This 'ubiquitin code' determine ...

    The post-translational modification of proteins with polyubiquitin regulates virtually all aspects of cell biology. Eight distinct chain linkage types co-exist in polyubiquitin and are independently regulated in cells. This 'ubiquitin code' determines the fate of the modified protein. Deubiquitinating enzymes of the ovarian tumour (OTU) family regulate cellular signalling by targeting distinct linkage types within polyubiquitin, and understanding their mechanisms of linkage specificity gives fundamental insights into the ubiquitin system. Here we reveal how the deubiquitinase Cezanne (also known as OTUD7B) specifically targets Lys11-linked polyubiquitin. Crystal structures of Cezanne alone and in complex with monoubiquitin and Lys11-linked diubiquitin, in combination with hydrogen-deuterium exchange mass spectrometry, enable us to reconstruct the enzymatic cycle in great detail. An intricate mechanism of ubiquitin-assisted conformational changes activates the enzyme, and while all chain types interact with the enzymatic S1 site, only Lys11-linked chains can bind productively across the active site and stimulate catalytic turnover. Our work highlights the plasticity of deubiquitinases and indicates that new conformational states can occur when a true substrate, such as diubiquitin, is bound at the active site.


    Organizational Affiliation

    Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factor alpha-induced protein 3
A, C
371Homo sapiensMutation(s): 0 
Gene Names: TNFAIP3 (OTUD7C)
EC: 2.3.2.-, 3.4.19.12
Find proteins for P21580 (Homo sapiens)
Go to Gene View: TNFAIP3
Go to UniProtKB:  P21580
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-B
B, D
76Homo sapiensMutation(s): 1 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factor alpha-induced protein 3
E, F
371Homo sapiensMutation(s): 0 
Gene Names: TNFAIP3 (OTUD7C)
EC: 2.3.2.-, 3.4.19.12
Find proteins for P21580 (Homo sapiens)
Go to Gene View: TNFAIP3
Go to UniProtKB:  P21580
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
AYE
Query on AYE
B, D
NON-POLYMERC3 H7 N

--

CSD
Query on CSD
E, F
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 64.195α = 90.00
b = 71.950β = 94.64
c = 203.926γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
Aimlessdata scaling
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomU105192732
European Research CouncilUnited Kingdom309756

Revision History 

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2016-10-26
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence